Reducing the Impacts of Hydroelectric Dams on Juvenile Anadromous Fishes: Bioengineering Evaluations Using Acoustic Imaging in the Columbia River, USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Gary E.; Ploskey, Gene R.; Hedgepeth, J.

2008-07-29

Dams impact the survival of juvenile anadromous fishes by obstructing migration corridors, lowering water quality, delaying migrations, and entraining fish in turbine discharge. To reduce these impacts, structural and operational modifications to dams— such as voluntary spill discharge, turbine intake guidance screens, and surface flow outlets—are instituted. Over the last six years, we have used acoustic imaging technology to evaluate the effects of these modifications on fish behavior, passage rates, entrainment zones, and fish/flow relationships at hydroelectric projects on the Columbia River. The imaging technique has evolved from studies documenting simple movement patterns to automated tracking of images to mergingmore » and analysis with concurrent hydraulic data. This chapter chronicles this evolution and shows how the information gleaned from the scientific evaluations has been applied to improve passage conditions for juvenile salmonids. We present data from Bonneville and The Dalles dams that document fish behavior and entrainment zones at sluiceway outlets (14 to 142 m3/s), fish passage rates through a gap at a turbine intake screen, and the relationship between fish swimming effort and hydraulic conditions. Dam operators and fisheries managers have applied these data to support decisions on operational and structural changes to the dams for the benefit of anadromous fish populations in the Columbia River basin.« less

Fully Automated Fluorescent in situ Hybridization (FISH) Staining and Digital Analysis of HER2 in Breast Cancer: A Validation Study

PubMed Central

van der Logt, Elise M. J.; Kuperus, Deborah A. J.; van Setten, Jan W.; van den Heuvel, Marius C.; Boers, James. E.; Schuuring, Ed; Kibbelaar, Robby E.

2015-01-01

HER2 assessment is routinely used to select patients with invasive breast cancer that might benefit from HER2-targeted therapy. The aim of this study was to validate a fully automated in situ hybridization (ISH) procedure that combines the automated Leica HER2 fluorescent ISH system for Bond with supervised automated analysis with the Visia imaging D-Sight digital imaging platform. HER2 assessment was performed on 328 formalin-fixed/paraffin-embedded invasive breast cancer tumors on tissue microarrays (TMA) and 100 (50 selected IHC 2+ and 50 random IHC scores) full-sized slides of resections/biopsies obtained for diagnostic purposes previously. For digital analysis slides were pre-screened at 20x and 100x magnification for all fluorescent signals and supervised-automated scoring was performed on at least two pictures (in total at least 20 nuclei were counted) with the D-Sight HER2 FISH analysis module by two observers independently. Results were compared to data obtained previously with the manual Abbott FISH test. The overall agreement with Abbott FISH data among TMA samples and 50 selected IHC 2+ cases was 98.8% (κ = 0.94) and 93.8% (κ = 0.88), respectively. The results of 50 additionally tested unselected IHC cases were concordant with previously obtained IHC and/or FISH data. The combination of the Leica FISH system with the D-Sight digital imaging platform is a feasible method for HER2 assessment in routine clinical practice for patients with invasive breast cancer. PMID:25844540

[Development of an original computer program FISHMet: use for molecular cytogenetic diagnosis and genome mapping by fluorescent in situ hybridization (FISH)].

PubMed

Iurov, Iu B; Khazatskiĭ, I A; Akindinov, V A; Dovgilov, L V; Kobrinskiĭ, B A; Vorsanova, S G

2000-08-01

Original software FISHMet has been developed and tried for improving the efficiency of diagnosis of hereditary diseases caused by chromosome aberrations and for chromosome mapping by fluorescent in situ hybridization (FISH) method. The program allows creation and analysis of pseudocolor chromosome images and hybridization signals in the Windows 95 system, allows computer analysis and editing of the results of pseudocolor hybridization in situ, including successive imposition of initial black-and-white images created using fluorescent filters (blue, green, and red), and editing of each image individually or of a summary pseudocolor image in BMP, TIFF, and JPEG formats. Components of image computer analysis system (LOMO, Leitz Ortoplan, and Axioplan fluorescent microscopes, COHU 4910 and Sanyo VCB-3512P CCD cameras, Miro-Video, Scion LG-3 and VG-5 image capture maps, and Pentium 100 and Pentium 200 computers) and specialized software for image capture and visualization (Scion Image PC and Video-Cup) have been used with good results in the study.

Membrane connectivity estimated by digital image analysis of HER2 immunohistochemistry is concordant with visual scoring and fluorescence in situ hybridization results: algorithm evaluation on breast cancer tissue microarrays

PubMed Central

2011-01-01

Introduction The human epidermal growth factor receptor 2 (HER2) is an established biomarker for management of patients with breast cancer. While conventional testing of HER2 protein expression is based on semi-quantitative visual scoring of the immunohistochemistry (IHC) result, efforts to reduce inter-observer variation and to produce continuous estimates of the IHC data are potentiated by digital image analysis technologies. Methods HER2 IHC was performed on the tissue microarrays (TMAs) of 195 patients with an early ductal carcinoma of the breast. Digital images of the IHC slides were obtained by Aperio ScanScope GL Slide Scanner. Membrane connectivity algorithm (HER2-CONNECT™, Visiopharm) was used for digital image analysis (DA). A pathologist evaluated the images on the screen twice (visual evaluations: VE1 and VE2). HER2 fluorescence in situ hybridization (FISH) was performed on the corresponding sections of the TMAs. The agreement between the IHC HER2 scores, obtained by VE1, VE2, and DA was tested for individual TMA spots and patient's maximum TMA spot values (VE1max, VE2max, DAmax). The latter were compared with the FISH data. Correlation of the continuous variable of the membrane connectivity estimate with the FISH data was tested. Results The pathologist intra-observer agreement (VE1 and VE2) on HER2 IHC score was almost perfect: kappa 0.91 (by spot) and 0.88 (by patient). The agreement between visual evaluation and digital image analysis was almost perfect at the spot level (kappa 0.86 and 0.87, with VE1 and VE2 respectively) and at the patient level (kappa 0.80 and 0.86, with VE1max and VE2max, respectively). The DA was more accurate than VE in detection of FISH-positive patients by recruiting 3 or 2 additional FISH-positive patients to the IHC score 2+ category from the IHC 0/1+ category by VE1max or VE2max, respectively. The DA continuous variable of the membrane connectivity correlated with the FISH data (HER2 and CEP17 copy numbers, and HER2/CEP17 ratio). Conclusion HER2 IHC digital image analysis based on membrane connectivity estimate was in almost perfect agreement with the visual evaluation of the pathologist and more accurate in detection of HER2 FISH-positive patients. Most immediate benefit of integrating the DA algorithm into the routine pathology HER2 testing may be obtained by alerting/reassuring pathologists of potentially misinterpreted IHC 0/1+ versus 2+ cases. PMID:21943197

Membrane connectivity estimated by digital image analysis of HER2 immunohistochemistry is concordant with visual scoring and fluorescence in situ hybridization results: algorithm evaluation on breast cancer tissue microarrays.

PubMed

Laurinaviciene, Aida; Dasevicius, Darius; Ostapenko, Valerijus; Jarmalaite, Sonata; Lazutka, Juozas; Laurinavicius, Arvydas

2011-09-23

The human epidermal growth factor receptor 2 (HER2) is an established biomarker for management of patients with breast cancer. While conventional testing of HER2 protein expression is based on semi-quantitative visual scoring of the immunohistochemistry (IHC) result, efforts to reduce inter-observer variation and to produce continuous estimates of the IHC data are potentiated by digital image analysis technologies. HER2 IHC was performed on the tissue microarrays (TMAs) of 195 patients with an early ductal carcinoma of the breast. Digital images of the IHC slides were obtained by Aperio ScanScope GL Slide Scanner. Membrane connectivity algorithm (HER2-CONNECT, Visiopharm) was used for digital image analysis (DA). A pathologist evaluated the images on the screen twice (visual evaluations: VE1 and VE2). HER2 fluorescence in situ hybridization (FISH) was performed on the corresponding sections of the TMAs. The agreement between the IHC HER2 scores, obtained by VE1, VE2, and DA was tested for individual TMA spots and patient's maximum TMA spot values (VE1max, VE2max, DAmax). The latter were compared with the FISH data. Correlation of the continuous variable of the membrane connectivity estimate with the FISH data was tested. The pathologist intra-observer agreement (VE1 and VE2) on HER2 IHC score was almost perfect: kappa 0.91 (by spot) and 0.88 (by patient). The agreement between visual evaluation and digital image analysis was almost perfect at the spot level (kappa 0.86 and 0.87, with VE1 and VE2 respectively) and at the patient level (kappa 0.80 and 0.86, with VE1max and VE2max, respectively). The DA was more accurate than VE in detection of FISH-positive patients by recruiting 3 or 2 additional FISH-positive patients to the IHC score 2+ category from the IHC 0/1+ category by VE1max or VE2max, respectively. The DA continuous variable of the membrane connectivity correlated with the FISH data (HER2 and CEP17 copy numbers, and HER2/CEP17 ratio). HER2 IHC digital image analysis based on membrane connectivity estimate was in almost perfect agreement with the visual evaluation of the pathologist and more accurate in detection of HER2 FISH-positive patients. Most immediate benefit of integrating the DA algorithm into the routine pathology HER2 testing may be obtained by alerting/reassuring pathologists of potentially misinterpreted IHC 0/1+ versus 2+ cases.

Quantification of human epidermal growth factor receptor 2 immunohistochemistry using the Ventana Image Analysis System: correlation with gene amplification by fluorescence in situ hybridization: the importance of instrument validation for achieving high (>95%) concordance rate.

PubMed

Dennis, Jake; Parsa, Rezvaneh; Chau, Donnie; Koduru, Prasad; Peng, Yan; Fang, Yisheng; Sarode, Venetia Rumnong

2015-05-01

The use of computer-based image analysis for scoring human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) has gained a lot of interest recently. We investigated the performance of the Ventana Image Analysis System (VIAS) in HER2 quantification by IHC and its correlation with fluorescence in situ hybridization (FISH). We specifically compared the 3+ IHC results using the manufacturer's machine score cutoffs versus laboratory-defined cutoffs with the FISH assay. Using the manufacturer's 3+ cutoff (VIAS score; 2.51 to 3.5), 181/536 (33.7%) were scored 3+, and FISH was positive in 147/181 (81.2%), 2 (1.1%) were equivocal, and 32 (17.6%) were FISH (-). Using the laboratory-defined 3+ cutoff (VIAS score 3.5), 52 (28.7%) cases were downgraded to 2+, of which 29 (55.7%) were FISH (-), and 23 (44.2%) were FISH (+). With the revised cutoff, there were improvements in the concordance rate from 89.1% to 97.0% and in the positive predictive value from 82.1% to 97.6%. The false-positive rate for 3+ decreased from 9.0% to 0.8%. Six of 175 (3.4%) IHC (-) cases were FISH (+). Three cases with a VIAS score 3.5 showed polysomy of chromosome 17. In conclusion, the VIAS may be a valuable tool for assisting pathologists in HER2 scoring; however, the positive cutoff defined by the manufacturer is associated with a high false-positive rate. This study highlights the importance of instrument validation/calibration to reduce false-positive results.

Utility of cytopathological specimens and an automated image analysis for the evaluation of HER2 status and intratumor heterogeneity in breast carcinoma.

PubMed

Arihiro, Koji; Oda, Miyo; Ogawa, Katsunari; Kaneko, Yoshie; Shimizu, Tomomi; Tanaka, Yuna; Marubashi, Yukari; Ishida, Katsunari; Takai, Chikako; Taoka, Chie; Kimura, Shuji; Shiroma, Noriyuki

2016-12-01

Although updated HER2 testing guidelines have been improved by a collaboration between the American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP) in 2013, HER2 evaluation is still problematic because of issues involving CEP17 polysomy, heterogeneity, and HER2 score 2+ cases. The aim of this retrospective study was to evaluate the relationship between HER2 gene heterogeneity, or so called CEP17 polysomy, using breast carcinoma cells sampled by scraping and the IHC score graded by automated image analysis using whole slide image. We randomly selected 23 breast carcinoma cases with a HER2 score 0, 24 cases with a HER2 score 1+, 24 cases with HER2 score 2+, and 23 cases with HER2 score 3+ from the records of patients with breast cancer at Hiroshima University Hospital. We compared the results of fluorescent in situ hybridization (FISH) using formalin-fixed, paraffin-embedded (FFPE) tissues and cytological samples and compared the HER2 score calculated using an automated image analysis using wholly scanned slide images and visual counting. We successfully performed the FISH assay in 78 of 94 cases (83%) using FFPE tissues and in all 94 (100%) cases using cytological samples. Frequency of both HER2 amplification and CEP17 polysomy was higher when cytological samples were used than when FFPE tissue was used. Frequency of HER2 heterogeneity using cytological samples was higher that than using FFPE tissue, except for the IHC score 3+ cases. When assessment of HER2 status based on FISH using FFPE tissue cannot be accomplished, FISH using cytological samples should be considered. When intensity of HER2 is heterogeneous in the tumor tissue, particularly in cases regarded as score 2+, they should be evaluated by automated image analysis using the whole slide image. Copyright © 2016 Elsevier GmbH. All rights reserved.

Semantic segmentation of mFISH images using convolutional networks.

PubMed

Pardo, Esteban; Morgado, José Mário T; Malpica, Norberto

2018-04-30

Multicolor in situ hybridization (mFISH) is a karyotyping technique used to detect major chromosomal alterations using fluorescent probes and imaging techniques. Manual interpretation of mFISH images is a time consuming step that can be automated using machine learning; in previous works, pixel or patch wise classification was employed, overlooking spatial information which can help identify chromosomes. In this work, we propose a fully convolutional semantic segmentation network for the interpretation of mFISH images, which uses both spatial and spectral information to classify each pixel in an end-to-end fashion. The semantic segmentation network developed was tested on samples extracted from a public dataset using cross validation. Despite having no labeling information of the image it was tested on, our algorithm yielded an average correct classification ratio (CCR) of 87.41%. Previously, this level of accuracy was only achieved with state of the art algorithms when classifying pixels from the same image in which the classifier has been trained. These results provide evidence that fully convolutional semantic segmentation networks may be employed in the computer aided diagnosis of genetic diseases with improved performance over the current image analysis methods. © 2018 International Society for Advancement of Cytometry. © 2018 International Society for Advancement of Cytometry.

A panoramic imaging system based on fish-eye lens

NASA Astrophysics Data System (ADS)

Wang, Ye; Hao, Chenyang

2017-10-01

Panoramic imaging has been closely watched as one of the major technologies of AR and VR. Mainstream panoramic imaging techniques lenses include fish-eye lenses, image splicing, and catadioptric imaging system. Meanwhile, fish-eyes are widely used in the big picture video surveillance. The advantage of fish-eye lenses is that they are easy to operate and cost less, but how to solve the image distortion of fish-eye lenses has always been a very important topic. In this paper, the image calibration algorithm of fish-eye lens is studied by comparing the method of interpolation, bilinear interpolation and double three interpolation, which are used to optimize the images.

Multifractal-based nuclei segmentation in fish images.

PubMed

Reljin, Nikola; Slavkovic-Ilic, Marijeta; Tapia, Coya; Cihoric, Nikola; Stankovic, Srdjan

2017-09-01

The method for nuclei segmentation in fluorescence in-situ hybridization (FISH) images, based on the inverse multifractal analysis (IMFA) is proposed. From the blue channel of the FISH image in RGB format, the matrix of Holder exponents, with one-by-one correspondence with the image pixels, is determined first. The following semi-automatic procedure is proposed: initial nuclei segmentation is performed automatically from the matrix of Holder exponents by applying predefined hard thresholding; then the user evaluates the result and is able to refine the segmentation by changing the threshold, if necessary. After successful nuclei segmentation, the HER2 (human epidermal growth factor receptor 2) scoring can be determined in usual way: by counting red and green dots within segmented nuclei, and finding their ratio. The IMFA segmentation method is tested over 100 clinical cases, evaluated by skilled pathologist. Testing results show that the new method has advantages compared to already reported methods.

Imaging of Chromosome Dynamics in Mouse Testis Tissue by Immuno-FISH.

PubMed

Scherthan, Harry

2017-01-01

The mouse (Mus musculus) represents the central mammalian genetic model system for biomedical and developmental research. Mutant mouse models have provided important insights into chromosome dynamics during the complex meiotic differentiation program that compensates for the genome doubling at fertilization. Homologous chromosomes (homologues) undergo dynamic pairing and recombine during first meiotic prophase before they become partitioned into four haploid sets by two consecutive meiotic divisions that lack an intervening S-phase. Fluorescence in situ hybridization (FISH) has been instrumental in the visualization and imaging of the dynamic reshaping of chromosome territories and mobility during prophase I, in which meiotic telomeres were found to act as pacemakers for the chromosome pairing dance. FISH combined with immunofluorescence (IF) co-staining of nuclear proteins has been instrumental for the visualization and imaging of mammalian meiotic chromosome behavior. This chapter describes FISH and IF methods for the analysis of chromosome dynamics in nuclei of paraffin-embedded mouse testes. The techniques have proven useful for fresh and archived paraffin testis material of several mammalian species.

Comparative Performance Analysis of Support Vector Machine, Random Forest, Logistic Regression and k-Nearest Neighbours in Rainbow Trout (Oncorhynchus Mykiss) Classification Using Image-Based Features

PubMed Central

Císař, Petr; Labbé, Laurent; Souček, Pavel; Pelissier, Pablo; Kerneis, Thierry

2018-01-01

The main aim of this study was to develop a new objective method for evaluating the impacts of different diets on the live fish skin using image-based features. In total, one-hundred and sixty rainbow trout (Oncorhynchus mykiss) were fed either a fish-meal based diet (80 fish) or a 100% plant-based diet (80 fish) and photographed using consumer-grade digital camera. Twenty-three colour features and four texture features were extracted. Four different classification methods were used to evaluate fish diets including Random forest (RF), Support vector machine (SVM), Logistic regression (LR) and k-Nearest neighbours (k-NN). The SVM with radial based kernel provided the best classifier with correct classification rate (CCR) of 82% and Kappa coefficient of 0.65. Although the both LR and RF methods were less accurate than SVM, they achieved good classification with CCR 75% and 70% respectively. The k-NN was the least accurate (40%) classification model. Overall, it can be concluded that consumer-grade digital cameras could be employed as the fast, accurate and non-invasive sensor for classifying rainbow trout based on their diets. Furthermore, these was a close association between image-based features and fish diet received during cultivation. These procedures can be used as non-invasive, accurate and precise approaches for monitoring fish status during the cultivation by evaluating diet’s effects on fish skin. PMID:29596375

Comparative Performance Analysis of Support Vector Machine, Random Forest, Logistic Regression and k-Nearest Neighbours in Rainbow Trout (Oncorhynchus Mykiss) Classification Using Image-Based Features.

PubMed

Saberioon, Mohammadmehdi; Císař, Petr; Labbé, Laurent; Souček, Pavel; Pelissier, Pablo; Kerneis, Thierry

2018-03-29

The main aim of this study was to develop a new objective method for evaluating the impacts of different diets on the live fish skin using image-based features. In total, one-hundred and sixty rainbow trout ( Oncorhynchus mykiss ) were fed either a fish-meal based diet (80 fish) or a 100% plant-based diet (80 fish) and photographed using consumer-grade digital camera. Twenty-three colour features and four texture features were extracted. Four different classification methods were used to evaluate fish diets including Random forest (RF), Support vector machine (SVM), Logistic regression (LR) and k -Nearest neighbours ( k -NN). The SVM with radial based kernel provided the best classifier with correct classification rate (CCR) of 82% and Kappa coefficient of 0.65. Although the both LR and RF methods were less accurate than SVM, they achieved good classification with CCR 75% and 70% respectively. The k -NN was the least accurate (40%) classification model. Overall, it can be concluded that consumer-grade digital cameras could be employed as the fast, accurate and non-invasive sensor for classifying rainbow trout based on their diets. Furthermore, these was a close association between image-based features and fish diet received during cultivation. These procedures can be used as non-invasive, accurate and precise approaches for monitoring fish status during the cultivation by evaluating diet's effects on fish skin.

Development of software and modification of Q-FISH protocol for estimation of individual telomere length in immunopathology.

PubMed

Barkovskaya, M Sh; Bogomolov, A G; Knauer, N Yu; Rubtsov, N B; Kozlov, V A

2017-04-01

Telomere length is an important indicator of proliferative cell history and potential. Decreasing telomere length in the cells of an immune system can indicate immune aging in immune-mediated and chronic inflammatory diseases. Quantitative fluorescent in situ hybridization (Q-FISH) of a labeled (C 3 TA[Formula: see text] peptide nucleic acid probe onto fixed metaphase cells followed by digital image microscopy allows the evaluation of telomere length in the arms of individual chromosomes. Computer-assisted analysis of microscopic images can provide quantitative information on the number of telomeric repeats in individual telomeres. We developed new software to estimate telomere length. The MeTeLen software contains new options that can be used to solve some Q-FISH and microscopy problems, including correction of irregular light effects and elimination of background fluorescence. The identification and description of chromosomes and chromosome regions are essential to the Q-FISH technique. To improve the quality of cytogenetic analysis after Q-FISH, we optimized the temperature and time of DNA-denaturation to get better DAPI-banding of metaphase chromosomes. MeTeLen was tested by comparing telomere length estimations for sister chromatids, background fluorescence estimations, and correction of nonuniform light effects. The application of the developed software for analysis of telomere length in patients with rheumatoid arthritis was demonstrated.

Color change of the snapper (Pagrus auratus) and Gurnard (Chelidonichthys kumu) skin and eyes during storage: effect of light polarization and contact with ice.

PubMed

Balaban, Murat O; Stewart, Kelsie; Fletcher, Graham C; Alçiçek, Zayde

2014-12-01

Ten gurnard and 10 snapper were stored on ice. One side always contacted the ice; the other side was always exposed to air. At different intervals for up to 12 d, the fish were placed in a light box, and the images of both sides were taken using polarized and nonpolarized illumination. Image analysis resulted in average L*, a*, and b* values of skin, and average L* values of the eyes. The skin L* value of gurnard changed significantly over time while that of snapper was substantially constant. The a* and b* values of both fish decreased over time. The L* values of eyes were significantly lower for polarized images, and significantly lower for the side of fish exposed to air only. This may be a concern in quality evaluation methods such as QIM. The difference of colors between the polarized and nonpolarized images was calculated to quantify the reflection off the surface of fish. For accurate measurement of surface color and eye color, use of polarized light is recommended. © 2014 Institute of Food Technologists®

smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability.

PubMed

Tsanov, Nikolay; Samacoits, Aubin; Chouaib, Racha; Traboulsi, Abdel-Meneem; Gostan, Thierry; Weber, Christian; Zimmer, Christophe; Zibara, Kazem; Walter, Thomas; Peter, Marion; Bertrand, Edouard; Mueller, Florian

2016-12-15

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification approach that uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide. The gene-specific probes are unlabelled and can therefore be synthesized at low cost, thus allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency. smiFISH is also flexible since differently labelled secondary detector probes can be used with the same primary probes. We demonstrate that this flexibility allows multicolor labelling without the need to synthesize new probe sets. We further demonstrate that the use of a specific acrydite detector oligonucleotide allows smiFISH to be combined with expansion microscopy, enabling the resolution of transcripts in 3D below the diffraction limit on a standard microscope. Lastly, we provide improved, fully automated software tools from probe-design to quantitative analysis of smFISH images. In short, we provide a complete workflow to obtain automatically counts of individual RNA molecules in single cells. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples.

PubMed

Zhou, Zhi; Pons, Marie Noëlle; Raskin, Lutgarde; Zilles, Julie L

2007-05-01

When fluorescence in situ hybridization (FISH) analyses are performed with complex environmental samples, difficulties related to the presence of microbial cell aggregates and nonuniform background fluorescence are often encountered. The objective of this study was to develop a robust and automated quantitative FISH method for complex environmental samples, such as manure and soil. The method and duration of sample dispersion were optimized to reduce the interference of cell aggregates. An automated image analysis program that detects cells from 4',6'-diamidino-2-phenylindole (DAPI) micrographs and extracts the maximum and mean fluorescence intensities for each cell from corresponding FISH images was developed with the software Visilog. Intensity thresholds were not consistent even for duplicate analyses, so alternative ways of classifying signals were investigated. In the resulting method, the intensity data were divided into clusters using fuzzy c-means clustering, and the resulting clusters were classified as target (positive) or nontarget (negative). A manual quality control confirmed this classification. With this method, 50.4, 72.1, and 64.9% of the cells in two swine manure samples and one soil sample, respectively, were positive as determined with a 16S rRNA-targeted bacterial probe (S-D-Bact-0338-a-A-18). Manual counting resulted in corresponding values of 52.3, 70.6, and 61.5%, respectively. In two swine manure samples and one soil sample 21.6, 12.3, and 2.5% of the cells were positive with an archaeal probe (S-D-Arch-0915-a-A-20), respectively. Manual counting resulted in corresponding values of 22.4, 14.0, and 2.9%, respectively. This automated method should facilitate quantitative analysis of FISH images for a variety of complex environmental samples.

A new colorimetrically-calibrated automated video-imaging protocol for day-night fish counting at the OBSEA coastal cabled observatory.

PubMed

del Río, Joaquín; Aguzzi, Jacopo; Costa, Corrado; Menesatti, Paolo; Sbragaglia, Valerio; Nogueras, Marc; Sarda, Francesc; Manuèl, Antoni

2013-10-30

Field measurements of the swimming activity rhythms of fishes are scant due to the difficulty of counting individuals at a high frequency over a long period of time. Cabled observatory video monitoring allows such a sampling at a high frequency over unlimited periods of time. Unfortunately, automation for the extraction of biological information (i.e., animals' visual counts per unit of time) is still a major bottleneck. In this study, we describe a new automated video-imaging protocol for the 24-h continuous counting of fishes in colorimetrically calibrated time-lapse photographic outputs, taken by a shallow water (20 m depth) cabled video-platform, the OBSEA. The spectral reflectance value for each patch was measured between 400 to 700 nm and then converted into standard RGB, used as a reference for all subsequent calibrations. All the images were acquired within a standardized Region Of Interest (ROI), represented by a 2 × 2 m methacrylate panel, endowed with a 9-colour calibration chart, and calibrated using the recently implemented "3D Thin-Plate Spline" warping approach in order to numerically define color by its coordinates in n-dimensional space. That operation was repeated on a subset of images, 500 images as a training set, manually selected since acquired under optimum visibility conditions. All images plus those for the training set were ordered together through Principal Component Analysis allowing the selection of 614 images (67.6%) out of 908 as a total corresponding to 18 days (at 30 min frequency). The Roberts operator (used in image processing and computer vision for edge detection) was used to highlights regions of high spatial colour gradient corresponding to fishes' bodies. Time series in manual and visual counts were compared together for efficiency evaluation. Periodogram and waveform analysis outputs provided very similar results, although quantified parameters in relation to the strength of respective rhythms were different. Results indicate that automation efficiency is limited by optimum visibility conditions. Data sets from manual counting present the larger day-night fluctuations in comparison to those derived from automation. This comparison indicates that the automation protocol subestimate fish numbers but it is anyway suitable for the study of community activity rhythms.

A New Colorimetrically-Calibrated Automated Video-Imaging Protocol for Day-Night Fish Counting at the OBSEA Coastal Cabled Observatory

PubMed Central

del Río, Joaquín; Aguzzi, Jacopo; Costa, Corrado; Menesatti, Paolo; Sbragaglia, Valerio; Nogueras, Marc; Sarda, Francesc; Manuèl, Antoni

2013-01-01

Field measurements of the swimming activity rhythms of fishes are scant due to the difficulty of counting individuals at a high frequency over a long period of time. Cabled observatory video monitoring allows such a sampling at a high frequency over unlimited periods of time. Unfortunately, automation for the extraction of biological information (i.e., animals' visual counts per unit of time) is still a major bottleneck. In this study, we describe a new automated video-imaging protocol for the 24-h continuous counting of fishes in colorimetrically calibrated time-lapse photographic outputs, taken by a shallow water (20 m depth) cabled video-platform, the OBSEA. The spectral reflectance value for each patch was measured between 400 to 700 nm and then converted into standard RGB, used as a reference for all subsequent calibrations. All the images were acquired within a standardized Region Of Interest (ROI), represented by a 2 × 2 m methacrylate panel, endowed with a 9-colour calibration chart, and calibrated using the recently implemented “3D Thin-Plate Spline” warping approach in order to numerically define color by its coordinates in n-dimensional space. That operation was repeated on a subset of images, 500 images as a training set, manually selected since acquired under optimum visibility conditions. All images plus those for the training set were ordered together through Principal Component Analysis allowing the selection of 614 images (67.6%) out of 908 as a total corresponding to 18 days (at 30 min frequency). The Roberts operator (used in image processing and computer vision for edge detection) was used to highlights regions of high spatial colour gradient corresponding to fishes' bodies. Time series in manual and visual counts were compared together for efficiency evaluation. Periodogram and waveform analysis outputs provided very similar results, although quantified parameters in relation to the strength of respective rhythms were different. Results indicate that automation efficiency is limited by optimum visibility conditions. Data sets from manual counting present the larger day-night fluctuations in comparison to those derived from automation. This comparison indicates that the automation protocol subestimate fish numbers but it is anyway suitable for the study of community activity rhythms. PMID:24177726

Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

PubMed

Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

1996-10-01

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription.

PubMed

Lee, Jinwoo; Foong, Yee Hoon; Musaitif, Ibrahim; Tong, Tiegang; Jefcoate, Colin

2016-07-05

The steroidogenic acute regulatory protein (StAR) has been proposed to serve as the switch that can turn on/off steroidogenesis. We investigated the events that facilitate dynamic StAR transcription in response to cAMP stimulation in MA-10 Leydig cells, focusing on splicing anomalies at StAR gene loci. We used 3' reverse primers in a single reaction to respectively quantify StAR primary (p-RNA), spliced (sp-RNA/mRNA), and extended 3' untranslated region (UTR) transcripts, which were quantitatively imaged by high-resolution fluorescence in situ hybridization (FISH). This approach delivers spatio-temporal resolution of initiation and splicing at single StAR loci, and transfers individual mRNA molecules to cytoplasmic sites. Gene expression was biphasic, initially showing slow splicing, transitioning to concerted splicing. The alternative 3.5-kb mRNAs were distinguished through the use of extended 3'UTR probes, which exhibited distinctive mitochondrial distribution. Combining quantitative PCR and FISH enables imaging of localization of RNA expression and analysis of RNA processing rates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Rapid depth perception in hunting archerfish II. An analysis of potential cues.

PubMed

Reinel, Caroline P; Schuster, Stefan

2018-05-24

Based on the initial movement of falling prey hunting archerfish select a C-start that turns them right to where their prey is going to land and lends the speed to arrive simultaneously with prey. Our preceding study suggested that the information sampled in less than 100 ms also includes the initial height of falling prey. Here we examine which cues the fish might be using to gauge height so quickly. First, we show that binocular cues are not required: C-starts that either could or could not have used binocular information were equally fast and precise. Next, we explored whether the fish were using simplifying assumptions about the absolute size of their prey or its distance from a structured background. However, experiments with unexpected changes from the standard conditions failed to cause any errors. We then tested the hypothesis that the fish might infer depth from accommodation or from cues related to blurring in the image of their falling prey. However, the fish determined also the height of 'fake-flies' correctly, whose image could never be focused and whose combined size and degree of blurring should have mislead the fish. Our findings are not compatible with the view that the fish uses a flexible combination of cues. They also do not support the view that height is gauged relative to structures in the vicinity of starting prey. We suggest that the fish use an elaborate analysis of looming to rapidly gauge initial height. © 2018. Published by The Company of Biologists Ltd.

Consistent melanophore spot patterns allow long-term individual recognition of Atlantic salmon Salmo salar.

PubMed

Stien, L H; Nilsson, J; Bui, S; Fosseidengen, J E; Kristiansen, T S; Øverli, Ø; Folkedal, O

2017-12-01

The present study shows that permanent melanophore spot patterns in Atlantic salmon Salmo salar make it possible to use images of the operculum to keep track of individual fish over extended periods of their life history. Post-smolt S. salar (n = 246) were initially photographed at an average mass of 98 g and again 10 months later after rearing in a sea cage, at an average mass of 3088 g. Spots that were present initially remained and were the most overt (largest) 10 months later, while new and less overt spots had developed. Visual recognition of spot size and position showed that fish with at least four initial spots were relatively easy to identify, while identifying fish with less than four spots could be challenging. An automatic image analysis method was developed and shows potential for fast match processing of large numbers of fish. The current findings promote visual recognition of opercular spots as a welfare-friendly alternative to tagging in experiments involving salmonid fishes. © The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of The Fisheries Society of the British Isles.

Advances of FishNet towards a fully automatic monitoring system for fish migration

NASA Astrophysics Data System (ADS)

Kratzert, Frederik; Mader, Helmut

2017-04-01

Restoring the continuum of river networks, affected by anthropogenic constructions, is one of the main objectives of the Water Framework Directive. Regarding fish migration, fish passes are a widely used measure. Often the functionality of these fish passes needs to be assessed by monitoring. Over the last years, we developed a new semi-automatic monitoring system (FishCam) which allows the contact free observation of fish migration in fish passes through videos. The system consists of a detection tunnel, equipped with a camera, a motion sensor and artificial light sources, as well as a software (FishNet), which helps to analyze the video data. In its latest version, the software is capable of detecting and tracking objects in the videos as well as classifying them into "fish" and "no-fish" objects. This allows filtering out the videos containing at least one fish (approx. 5 % of all grabbed videos) and reduces the manual labor to the analysis of these videos. In this state the entire system has already been used in over 20 different fish passes across Austria for a total of over 140 months of monitoring resulting in more than 1.4 million analyzed videos. As a next step towards a fully automatic monitoring system, a key feature is the automatized classification of the detected fish into their species, which is still an unsolved task in a fully automatic monitoring environment. Recent advances in the field of machine learning, especially image classification with deep convolutional neural networks, sound promising in order to solve this problem. In this study, different approaches for the fish species classification are tested. Besides an image-only based classification approach using deep convolutional neural networks, various methods that combine the power of convolutional neural networks as image descriptors with additional features, such as the fish length and the time of appearance, are explored. To facilitate the development and testing phase of this approach, a subset of six fish species of Austrian rivers and streams is considered in this study. All scripts and the data to reproduce the results of this study will be made publicly available on GitHub* at the beginning of the EGU2017 General Assembly. * https://github.com/kratzert/EGU2017_public/

Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators.

PubMed

Chiao, Chuan-Chin; Wickiser, J Kenneth; Allen, Justine J; Genter, Brock; Hanlon, Roger T

2011-05-31

Camouflage is a widespread phenomenon throughout nature and an important antipredator tactic in natural selection. Many visual predators have keen color perception, and thus camouflage patterns should provide some degree of color matching in addition to other visual factors such as pattern, contrast, and texture. Quantifying camouflage effectiveness in the eyes of the predator is a challenge from the perspectives of both biology and optical imaging technology. Here we take advantage of hyperspectral imaging (HSI), which records full-spectrum light data, to simultaneously visualize color match and pattern match in the spectral and the spatial domains, respectively. Cuttlefish can dynamically camouflage themselves on any natural substrate and, despite their colorblindness, produce body patterns that appear to have high-fidelity color matches to the substrate when viewed directly by humans or with RGB images. Live camouflaged cuttlefish on natural backgrounds were imaged using HSI, and subsequent spectral analysis revealed that most reflectance spectra of individual cuttlefish and substrates were similar, rendering the color match possible. Modeling color vision of potential di- and trichromatic fish predators of cuttlefish corroborated the spectral match analysis and demonstrated that camouflaged cuttlefish show good color match as well as pattern match in the eyes of fish predators. These findings (i) indicate the strong potential of HSI technology to enhance studies of biological coloration and (ii) provide supporting evidence that cuttlefish can produce color-coordinated camouflage on natural substrates despite lacking color vision.

Analysis of brook trout spatial behavior during passage attempts in corrugated culverts using near-infrared illumination video imagery

USGS Publications Warehouse

Bergeron, Normand E.; Constantin, Pierre-Marc; Goerig, Elsa; Castro-Santos, Theodore R.

2016-01-01

We used video recording and near-infrared illumination to document the spatial behavior of brook trout of various sizes attempting to pass corrugated culverts under different hydraulic conditions. Semi-automated image analysis was used to digitize fish position at high temporal resolution inside the culvert, which allowed calculation of various spatial behavior metrics, including instantaneous ground and swimming speed, path complexity, distance from side walls, velocity preference ratio (mean velocity at fish lateral position/mean crosssectional velocity) as well as number and duration of stops in forward progression. The presentation summarizes the main results and discusses how they could be used to improve fish passage performance in culverts.

Registration of Panoramic/Fish-Eye Image Sequence and LiDAR Points Using Skyline Features

PubMed Central

Zhu, Ningning; Jia, Yonghong; Ji, Shunping

2018-01-01

We propose utilizing a rigorous registration model and a skyline-based method for automatic registration of LiDAR points and a sequence of panoramic/fish-eye images in a mobile mapping system (MMS). This method can automatically optimize original registration parameters and avoid the use of manual interventions in control point-based registration methods. First, the rigorous registration model between the LiDAR points and the panoramic/fish-eye image was built. Second, skyline pixels from panoramic/fish-eye images and skyline points from the MMS’s LiDAR points were extracted, relying on the difference in the pixel values and the registration model, respectively. Third, a brute force optimization method was used to search for optimal matching parameters between skyline pixels and skyline points. In the experiments, the original registration method and the control point registration method were used to compare the accuracy of our method with a sequence of panoramic/fish-eye images. The result showed: (1) the panoramic/fish-eye image registration model is effective and can achieve high-precision registration of the image and the MMS’s LiDAR points; (2) the skyline-based registration method can automatically optimize the initial attitude parameters, realizing a high-precision registration of a panoramic/fish-eye image and the MMS’s LiDAR points; and (3) the attitude correction values of the sequences of panoramic/fish-eye images are different, and the values must be solved one by one. PMID:29883431

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted frommore » a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.« less

Breast cancer evaluation by fluorescent dot detection using combined mathematical morphology and multifractal techniques

PubMed Central

2011-01-01

Background Fluorescence in situ hybridization (FISH) is very accurate method for measuring HER2 gene copies, as a sign of potential breast cancer. This method requires small tissue samples, and has a high sensitivity to detect abnormalities from a histological section. By using multiple colors, this method allows the detection of multiple targets simultaneously. The target parts in the cells become visible as colored dots. The HER-2 probes are visible as orange stained spots under a fluorescent microscope while probes for centromere 17 (CEP-17), the chromosome on which the gene HER-2/neu is located, are visible as green spots. Methods The conventional analysis involves the scoring of the ratio of HER-2/neu over CEP 17 dots within each cell nucleus and then averaging the scores for a number of 60 cells. A ratio of 2.0 of HER-2/neu to CEP 17 copy number denotes amplification. Several methods have been proposed for the detection and automated evaluation (dot counting) of FISH signals. In this paper the combined method based on the mathematical morphology (MM) and inverse multifractal (IMF) analysis is suggested. Similar method was applied recently in detection of microcalcifications in digital mammograms, and was very successful. Results The combined MM using top-hat and bottom-hat filters, and the IMF method was applied to FISH images from Molecular Biology Lab, Department of Pathology, Wielkoposka Cancer Center, Poznan. Initial results indicate that this method can be applied to FISH images for the evaluation of HER2/neu status. Conclusions Mathematical morphology and multifractal approach are used for colored dot detection and counting in FISH images. Initial results derived on clinical cases are promising. Note that the overlapping of colored dots, particularly red/orange dots, needs additional improvements in post-processing. PMID:21489192

Rapid detection of parasite in muscle fibers of fishes using a portable microscope imaging technique (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Jayoung; Lee, Hoonsoo; Kim, Moon S.; Cho, Byoungkwan

2017-05-01

Fishes are a widely used food material in the world. Recently about 4% of the fishes are infected with Kudoa thyrsites in Asian ocean. Kudoa thyrsites is a parasite that is found within the muscle fibers of fishes. The infected fishes can be a reason of food poisoning, which should be sorted out before distribution and consumption. Although Kudoa thyrsites is visible to the naked eye, it could be easily overlooked due to the micro-scale size and similar color with fish tissue. In addition, the visual inspection is labor intensive works resulting in loss of money and time. In this study, a portable microscopic camera was utilized to obtain images of raw fish slices. The optimized image processing techniques with polarized transmittance images provided reliable performance. The result shows that the portable microscopic imaging method can be used to detect parasites rapidly and non-destructively, which could be an alternative to manual inspections.

FISH analysis for diagnostic evaluation of challenging melanocytic lesions.

PubMed

Zimmermann, A K; Hirschmann, A; Pfeiffer, D; Paredes, B E; Diebold, J

2010-09-01

The differential diagnosis of malignant melanomas and atypical melanocytic nevi is still a diagnostic challenge. The currently accepted morphologic criteria show substantial interobserver variability, likewise immunohistochemical studies are often not able to discriminate these lesions reliably. Techniques that support diagnostic accuracy are of the greatest importance considering the growing incidence of malignant melanomas and their increase in younger patients. In this study we analyzed the feasibility of fluorescence in situ hybridization (FISH) analysis for the discrimination of malignant and benign melanocytic tumors. A panel of DNA probes was used to detect chromosomal aberrations of chromosomes 6 and 11. On a series of 5 clearly malignant and benign melanocytic tumors we confirmed the applicability of the test. Then we focused on examination of ambiguous melanocytic lesions, where atypical cells are often difficult to relocalize in the 4',6-Diamidino-2-phenylindol (DAPI)-fluorescence stain. FISH analyses were conducted on destained H&E-stained slides. By comparison of the DAPI-image with photos taken from the H&E stain, unambiguous assignment of the FISH results to the conspicuous groups of cells was possible. The results of FISH analysis were consistent with the conventional diagnosis in 11 of 14 small ambiguous lesions. Of the remaining 3 cases, 2 showed FISH-results close to the cut-off level. Comparison of FISH results on thin and thick sections revealed that the cut-off values have to be adapted for 2 microm destained sections. In conclusion, FISH analysis is a useful and applicable tool for assessment of even smallest melanocytic neoplasms, although there will remain unclear cases that cannot be solved even after additional FISH evaluation.

Swimming Performance of Toy Robotic Fish

NASA Astrophysics Data System (ADS)

Petelina, Nina; Mendelson, Leah; Techet, Alexandra

2015-11-01

HEXBUG AquaBotsTM are a commercially available small robot fish that come in a variety of ``species''. These models have varying caudal fin shapes and randomly-varied modes of swimming including forward locomotion, diving, and turning. In this study, we assess the repeatability and performance of the HEXBUG swimming behaviors and discuss the use of these toys to develop experimental techniques and analysis methods to study live fish swimming. In order to determine whether these simple, affordable model fish can be a valid representation for live fish movement, two models, an angelfish and a shark, were studied using 2D Particle Image Velocimetry (PIV) and 3D Synthetic Aperture PIV. In a series of experiments, the robotic fish were either allowed to swim freely or towed in one direction at a constant speed. The resultant measurements of the caudal fin wake are compared to data from previous studies of a real fish and simplified flapping propulsors.

Groping for quantitative digital 3-D image analysis: an approach to quantitative fluorescence in situ hybridization in thick tissue sections of prostate carcinoma.

PubMed

Rodenacker, K; Aubele, M; Hutzler, P; Adiga, P S

1997-01-01

In molecular pathology numerical chromosome aberrations have been found to be decisive for the prognosis of malignancy in tumours. The existence of such aberrations can be detected by interphase fluorescence in situ hybridization (FISH). The gain or loss of certain base sequences in the desoxyribonucleic acid (DNA) can be estimated by counting the number of FISH signals per cell nucleus. The quantitative evaluation of such events is a necessary condition for a prospective use in diagnostic pathology. To avoid occlusions of signals, the cell nucleus has to be analyzed in three dimensions. Confocal laser scanning microscopy is the means to obtain series of optical thin sections from fluorescence stained or marked material to fulfill the conditions mentioned above. A graphical user interface (GUI) to a software package for display, inspection, count and (semi-)automatic analysis of 3-D images for pathologists is outlined including the underlying methods of 3-D image interaction and segmentation developed. The preparative methods are briefly described. Main emphasis is given to the methodical questions of computer-aided analysis of large 3-D image data sets for pathologists. Several automated analysis steps can be performed for segmentation and succeeding quantification. However tumour material is in contrast to isolated or cultured cells even for visual inspection, a difficult material. For the present a fully automated digital image analysis of 3-D data is not in sight. A semi-automatic segmentation method is thus presented here.

QUANTITATIVE IMAGING AND STATISTICAL ANALYSIS OF FLUORESCENCE IN SITU HYBRIDIZATION (FISH) OF AUREOBASIDIUM PULLULANS. (R823845)

EPA Science Inventory

Abstract

Image and multifactorial statistical analyses were used to evaluate the intensity of fluorescence signal from cells of three strains of A. pullulans and one strain of Rhodosporidium toruloides, as an outgroup, hybridized with either a universal o...

Is there an association between flow diverter fish mouthing and delayed-type hypersensitivity to metals?-a case-control study.

PubMed

Kocer, Naci; Mondel, Prabath Kumar; Yamac, Elif; Kavak, Ayse; Kizilkilic, Osman; Islak, Civan

2017-11-01

Flow diverters are increasingly used in the treatment of complex and giant intracranial aneurysms. However, they are associated with complications like late aneurysmal rupture. Additionally, flow diverters show focal structural decrease in luminal diameter without any intimal hyperplasia. This resembles a "fish mouth" when viewed en face. In this pilot study, we tested the hypothesis of a possible association between flow diverter fish-mouthing and delayed-type hypersensitivity to its metal constituents. We retrospectively reviewed patient records from our center between May 2010 and November 2015. A total of nine patients had flow diverter fish mouthing. A control group of 25 patients was selected. All study participants underwent prospective patch test to detect hypersensitivity to flow diverter metal constituents. Analysis was performed using logistic regression analysis and Wilcoxon sign rank sum test. Univariate and multivariate analyses were performed to test variables to predict flow diverter fish mouthing. The association between flow diverter fish mouthing and positive patch test was not statistically significant. In multivariate analysis, history of allergy and maximum aneurysm size category was associated with flow diverter fish mouthing. This was further confirmed on Wilcoxon sign rank sum test. The study showed statistically significant association between flow diverter fish mouthing and history of contact allergy and a small aneurysmal size. Further large-scale studies are needed to detect a statistically significant association between flow diverter fish mouthing and patch test. We recommend early and more frequent follow-up imaging in patients with contact allergy to detect flow diverter fish mouthing and its subsequent evolution.

Experimental visualization of rapid maneuvering fish

NASA Astrophysics Data System (ADS)

Daigh, S.; Techet, A. H.

2003-11-01

A freshwater tropical fish, Danio aequippinatus, is studied undergoing rapid turning and fast starting maneuvers. This agile species of fish is ideal for this study as it is capable of quick turning and darting motions up to 5g's. The fgish studied are 4-5 cm in length. The speed and kinematics of the maneuvering is determined by video analysis. Planar and stereo Particle Image Velocimetry (PIV) is used to map the vortical patterns in the wake of the maneuvering fish. PIV visualizations reveal that during C-shaped maneuvers a ring shaped jet vortex is formed. Fast starting behavior is also presented. PIV data is used to approixmate the thrust vectoring force produced during each maneuver.

Using image analysis to predict the weight of Alaskan salmon of different species.

PubMed

Balaban, Murat O; Unal Sengör, Gülgün F; Gil Soriano, Mario; Guillén Ruiz, Elena

2010-04-01

After harvesting, salmon is sorted by species, size, and quality. This is generally manually done by operators. Automation would bring repeatability, objectivity, and record-keeping capabilities to these tasks. Machine vision (MV) and image analysis have been used in sorting many agricultural products. Four salmon species were tested: pink (Oncorhynchus gorbuscha), red (Oncorhynchus nerka), silver (Oncorhynchus kisutch), and chum (Oncorhynchus keta). A total of 60 whole fish from each species were first weighed, then placed in a light box to take their picture. Weight compared with view area as well as length and width correlations were developed. In addition the effect of "hump" development (see text) of pink salmon on this correlation was investigated. It was possible to predict the weight of a salmon by view area, regardless of species, and regardless of the development of a hump for pinks. Within pink salmon there was a small but insignificant difference between predictive equations for the weight of "regular" fish and "humpy" fish. Machine vision can accurately predict the weight of whole salmon for sorting.

[Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification].

PubMed

Bukharina, N S; Ivanov, Yu D; Pleshakova, T O; Frantsuzov, P A; Andreeva, E Yu; Kaysheva, A L; Izotov, A A; Pavlova, T I; Ziborov, V S; Radko, S P; Archakov, A I

2015-01-01

A method of atomic force microscopy-based fishing (AFM fishing) has been developed for protein detection in the analyte solution using a chip with an immobilized aptamer. This method is based on the biospecific fishing of a target protein from a bulk solution onto the small AFM chip area with the immobilized aptamer to this protein used as the molecular probe. Such aptamer-based approach allows to increase an AFM image contrast compared to the antibody-based approach. Mass spectrometry analysis used after the biospecific fishing to identify the target protein on the AFM chip has proved complex formation. Use of the AFM chip with the immobilized aptamer avoids interference of the antibody and target protein peaks in a mass spectrum.

Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis.

PubMed

Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J; Grau, Raúl; Barat, José M

2016-10-19

A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0-6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead's pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R² of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness.

Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis

PubMed Central

Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J.; Grau, Raúl; Barat, José M.

2016-01-01

A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0–6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead’s pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R2 of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness. PMID:27775556

An automated assay for the assessment of cardiac arrest in fish embryo.

PubMed

Puybareau, Elodie; Genest, Diane; Barbeau, Emilie; Léonard, Marc; Talbot, Hugues

2017-02-01

Studies on fish embryo models are widely developed in research. They are used in several research fields including drug discovery or environmental toxicology. In this article, we propose an entirely automated assay to detect cardiac arrest in Medaka (Oryzias latipes) based on image analysis. We propose a multi-scale pipeline based on mathematical morphology. Starting from video sequences of entire wells in 24-well plates, we focus on the embryo, detect its heart, and ascertain whether or not the heart is beating based on intensity variation analysis. Our image analysis pipeline only uses commonly available operators. It has a low computational cost, allowing analysis at the same rate as acquisition. From an initial dataset of 3192 videos, 660 were discarded as unusable (20.7%), 655 of them correctly so (99.25%) and only 5 incorrectly so (0.75%). The 2532 remaining videos were used for our test. On these, 45 errors were made, leading to a success rate of 98.23%. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spot counting on fluorescence in situ hybridization in suspension images using Gaussian mixture model

NASA Astrophysics Data System (ADS)

Liu, Sijia; Sa, Ruhan; Maguire, Orla; Minderman, Hans; Chaudhary, Vipin

2015-03-01

Cytogenetic abnormalities are important diagnostic and prognostic criteria for acute myeloid leukemia (AML). A flow cytometry-based imaging approach for FISH in suspension (FISH-IS) was established that enables the automated analysis of several log-magnitude higher number of cells compared to the microscopy-based approaches. The rotational positioning can occur leading to discordance between spot count. As a solution of counting error from overlapping spots, in this study, a Gaussian Mixture Model based classification method is proposed. The Akaike information criterion (AIC) and Bayesian information criterion (BIC) of GMM are used as global image features of this classification method. Via Random Forest classifier, the result shows that the proposed method is able to detect closely overlapping spots which cannot be separated by existing image segmentation based spot detection methods. The experiment results show that by the proposed method we can obtain a significant improvement in spot counting accuracy.

Automated microscopy system for detection and genetic characterization of fetal nucleated red blood cells on slides

NASA Astrophysics Data System (ADS)

Ravkin, Ilya; Temov, Vladimir

1998-04-01

The detection and genetic analysis of fetal cells in maternal blood will permit noninvasive prenatal screening for genetic defects. Applied Imaging has developed and is currently evaluating a system for semiautomatic detection of fetal nucleated red blood cells on slides and acquisition of their DNA probe FISH images. The specimens are blood smears from pregnant women (9 - 16 weeks gestation) enriched for nucleated red blood cells (NRBC). The cells are identified by using labeled monoclonal antibodies directed to different types of hemoglobin chains (gamma, epsilon); the nuclei are stained with DAPI. The Applied Imaging system has been implemented with both Olympus BX and Nikon Eclipse series microscopes which were equipped with transmission and fluorescence optics. The system includes the following motorized components: stage, focus, transmission, and fluorescence filter wheels. A video camera with light integration (COHU 4910) permits low light imaging. The software capabilities include scanning, relocation, autofocusing, feature extraction, facilities for operator review, and data analysis. Detection of fetal NRBCs is achieved by employing a combination of brightfield and fluorescence images of nuclear and cytoplasmic markers. The brightfield and fluorescence images are all obtained with a single multi-bandpass dichroic mirror. A Z-stack of DNA probe FISH images is acquired by moving focus and switching excitation filters. This stack is combined to produce an enhanced image for presentation and spot counting.

Cryptic Translocation Identification in Human and Mouse using Several Telomeric Multiplex FISH (TM-FISH) Strategies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henegariu, O; Artan, S; Greally, J M

2003-08-19

Experimental data published in recent years showed that up to 10% of all cases with mild to severe idiopathic mental retardation may result from small rearrangements of the subtelomeric regions of human chromosomes. To detect such cryptic translocations, we developed a ''telomeric'' multiplex FISH assay, using a set of previously published and commercially available subtelomeric probes. This set of probes includes 41 cosmid/PAC/P1 clones located from less than 100kb to about 1 Mb from the end of the chromosomes. Similarly, a published mouse probe set, comprised of BACs hybridizing to the closest known marker toward the centromere and telomere ofmore » each mouse chromosome, was used to develop a mouse-specific ''telomeric'' M-FISH. Three different combinatorial labeling strategies were used to simultaneously detect all human sub-telomeric regions on one slide. The simplest approach uses only three fluors, and can be performed in laboratories lacking sophisticated imaging equipment or personnel highly trained in cytogenetics. A standard fluorescence microscope equipped with only three filters is sufficient. Fluor-dUTPs and labeled probes can be custom-made, thus dramatically reducing costs. Images can be prepared using generic imaging software (Adobe Photoshop), and analysis performed by simple visual inspection.« less

Species composition and assemblages of ichthyoplankton during summer in the East China Sea

NASA Astrophysics Data System (ADS)

Lin, Han-Yang; Chiu, Mei-Yun; Shih, Yu-Ming; Chen, I.-Shiung; Lee, Ming-An; Shao, Kwang-Tsao

2016-09-01

The East China Sea (ECS) is one of the most important fish spawning and nursery grounds in the north Pacific. Even though summer is an important spawning season for many fishes in the region, large-scale molecular identification studies on ichthyoplankton during this season are few. In this study, we sampled 8,933 fish eggs and 12,161 fish larvae from 25 stations during the summer of 2009. Using DNA barcoding, a number of the fish eggs and larvae were identified and classified into 45 and 124 taxa, respectively. Principal component analysis (PCA) categorized the inshore stations of the Changjiang Diluted Water area as having the hydrographic features of low sea surface temperature (SST), salinity (SSS) and high chlorophyll a (SSC) contents, whereas the continental shelf and offshore stations under the influence of the Kuroshio Current displayed the opposite results. Ichthyoplankton was more abundant at the inshore stations than the offshore stations, but species diversity was lower at the former locations. Species compositions of both fish eggs and fish larvae at the 25 stations were categorized into three different assemblages based on a non-metric multidimensional scaling analysis. Combining the assemblage patterns of ichthyoplankton with the results of the PCA and satellite images of SST and SSC showed that the assemblage patterns of fish eggs were correlated with water mass, while those of the fish larvae were not.

Combining the genetic algorithm and successive projection algorithm for the selection of feature wavelengths to evaluate exudative characteristics in frozen-thawed fish muscle.

PubMed

Cheng, Jun-Hu; Sun, Da-Wen; Pu, Hongbin

2016-04-15

The potential use of feature wavelengths for predicting drip loss in grass carp fish, as affected by being frozen at -20°C for 24 h and thawed at 4°C for 1, 2, 4, and 6 days, was investigated. Hyperspectral images of frozen-thawed fish were obtained and their corresponding spectra were extracted. Least-squares support vector machine and multiple linear regression (MLR) models were established using five key wavelengths, selected by combining a genetic algorithm and successive projections algorithm, and this showed satisfactory performance in drip loss prediction. The MLR model with a determination coefficient of prediction (R(2)P) of 0.9258, and lower root mean square error estimated by a prediction (RMSEP) of 1.12%, was applied to transfer each pixel of the image and generate the distribution maps of exudation changes. The results confirmed that it is feasible to identify the feature wavelengths using variable selection methods and chemometric analysis for developing on-line multispectral imaging. Copyright © 2015 Elsevier Ltd. All rights reserved.

Glossiness and perishable food quality: visual freshness judgment of fish eyes based on luminance distribution.

PubMed

Murakoshi, Takuma; Masuda, Tomohiro; Utsumi, Ken; Tsubota, Kazuo; Wada, Yuji

2013-01-01

Previous studies have reported the effects of statistics of luminance distribution on visual freshness perception using pictures which included the degradation process of food samples. However, these studies did not examine the effect of individual differences between the same kinds of food. Here we elucidate whether luminance distribution would continue to have a significant effect on visual freshness perception even if visual stimuli included individual differences in addition to the degradation process of foods. We took pictures of the degradation of three fishes over 3.29 hours in a controlled environment, then cropped square patches of their eyes from the original images as visual stimuli. Eleven participants performed paired comparison tests judging the visual freshness of the fish eyes at three points of degradation. Perceived freshness scores (PFS) were calculated using the Bradley-Terry Model for each image. The ANOVA revealed that the PFS for each fish decreased as the degradation time increased; however, the differences in the PFS between individual fish was larger for the shorter degradation time, and smaller for the longer degradation time. A multiple linear regression analysis was conducted in order to determine the relative importance of the statistics of luminance distribution of the stimulus images in predicting PFS. The results show that standard deviation and skewness in luminance distribution have a significant influence on PFS. These results show that even if foodstuffs contain individual differences, visual freshness perception and changes in luminance distribution correlate with degradation time.

Semi-automated scoring of triple-probe FISH in human sperm using confocal microscopy.

PubMed

Branch, Francesca; Nguyen, GiaLinh; Porter, Nicholas; Young, Heather A; Martenies, Sheena E; McCray, Nathan; Deloid, Glen; Popratiloff, Anastas; Perry, Melissa J

2017-09-01

Structural and numerical sperm chromosomal aberrations result from abnormal meiosis and are directly linked to infertility. Any live births that arise from aneuploid conceptuses can result in syndromes such as Kleinfelter, Turners, XYY and Edwards. Multi-probe fluorescence in situ hybridization (FISH) is commonly used to study sperm aneuploidy, however manual FISH scoring in sperm samples is labor-intensive and introduces errors. Automated scoring methods are continuously evolving. One challenging aspect for optimizing automated sperm FISH scoring has been the overlap in excitation and emission of the fluorescent probes used to enumerate the chromosomes of interest. Our objective was to demonstrate the feasibility of combining confocal microscopy and spectral imaging with high-throughput methods for accurately measuring sperm aneuploidy. Our approach used confocal microscopy to analyze numerical chromosomal abnormalities in human sperm using enhanced slide preparation and rigorous semi-automated scoring methods. FISH for chromosomes X, Y, and 18 was conducted to determine sex chromosome disomy in sperm nuclei. Application of online spectral linear unmixing was used for effective separation of four fluorochromes while decreasing data acquisition time. Semi-automated image processing, segmentation, classification, and scoring were performed on 10 slides using custom image processing and analysis software and results were compared with manual methods. No significant differences in disomy frequencies were seen between the semi automated and manual methods. Samples treated with pepsin were observed to have reduced background autofluorescence and more uniform distribution of cells. These results demonstrate that semi-automated methods using spectral imaging on a confocal platform are a feasible approach for analyzing numerical chromosomal aberrations in sperm, and are comparable to manual methods. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Quality grading of Atlantic salmon (Salmo salar) by computer vision.

PubMed

Misimi, E; Erikson, U; Skavhaug, A

2008-06-01

In this study, we present a promising method of computer vision-based quality grading of whole Atlantic salmon (Salmo salar). Using computer vision, it was possible to differentiate among different quality grades of Atlantic salmon based on the external geometrical information contained in the fish images. Initially, before the image acquisition, the fish were subjectively graded and labeled into grading classes by a qualified human inspector in the processing plant. Prior to classification, the salmon images were segmented into binary images, and then feature extraction was performed on the geometrical parameters of the fish from the grading classes. The classification algorithm was a threshold-based classifier, which was designed using linear discriminant analysis. The performance of the classifier was tested by using the leave-one-out cross-validation method, and the classification results showed a good agreement between the classification done by human inspectors and by the computer vision. The computer vision-based method classified correctly 90% of the salmon from the data set as compared with the classification by human inspector. Overall, it was shown that computer vision can be used as a powerful tool to grade Atlantic salmon into quality grades in a fast and nondestructive manner by a relatively simple classifier algorithm. The low cost of implementation of today's advanced computer vision solutions makes this method feasible for industrial purposes in fish plants as it can replace manual labor, on which grading tasks still rely.

Development of Sorting System for Fishes by Feed-forward Neural Networks Using Rotation Invariant Features

NASA Astrophysics Data System (ADS)

Shiraishi, Yuhki; Takeda, Fumiaki

In this research, we have developed a sorting system for fishes, which is comprised of a conveyance part, a capturing image part, and a sorting part. In the conveyance part, we have developed an independent conveyance system in order to separate one fish from an intertwined group of fishes. After the image of the separated fish is captured in the capturing part, a rotation invariant feature is extracted using two-dimensional fast Fourier transform, which is the mean value of the power spectrum with the same distance from the origin in the spectrum field. After that, the fishes are classified by three-layered feed-forward neural networks. The experimental results show that the developed system classifies three kinds of fishes captured in various angles with the classification ratio of 98.95% for 1044 captured images of five fishes. The other experimental results show the classification ratio of 90.7% for 300 fishes by 10-fold cross validation method.

Novel method based on video tracking system for simultaneous measurement of kinematics and flow in the wake of a freely swimming fish

NASA Astrophysics Data System (ADS)

Wu, Guanhao; Yang, Yan; Zeng, Lijiang

2006-11-01

A novel method based on video tracking system for simultaneous measurement of kinematics and flow in the wake of a freely swimming fish is described. Spontaneous and continuous swimming behaviors of a variegated carp (Cyprinus carpio) are recorded by two cameras mounted on a translation stage which is controlled to track the fish. By processing the images recorded during tracking, the detailed kinematics based on calculated midlines and quantitative analysis of the flow in the wake during a low-speed turn and burst-and-coast swimming are revealed. We also draw the trajectory of the fish during a continuous swimming bout containing several moderate maneuvers. The results prove that our method is effective for studying maneuvers of fish both from kinematic and hydrodynamic viewpoints.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

DOE PAGES

Cui, Yi; Hu, Dehong; Markillie, Lye Meng; ...

2017-10-04

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Construct Abstraction for Automatic Information Abstraction from Digital Images

DTIC Science & Technology

2006-05-30

objects and features and the names of objects of objects and features. For example, in Figure 15 the parts of the fish could be named the ‘mouth... fish -1 fish -2 fish -3 tennis shoe tennis racquet...of abstraction and generality. For example, an algorithm might usefully find a polygon ( blob ) in an image and calculate numbers such as the

In Vivo Time-Lapse Imaging in the Zebrafish Lateral Line: A Flexible, Open-Ended Research Project for an Undergraduate Neurobiology Laboratory Course.

PubMed

Marra, Molly H; Tobias, Zachary J C; Cohen, Hannah R; Glover, Greta; Weissman, Tamily A

2015-01-01

The lateral line sensory system in fish detects movements in the water and allows fish to respond to predators, prey, and other stimuli. As the lateral line forms in the first two days of zebrafish development, axons extend caudally along the lateral surface of the fish, eventually forming synapses with hair cells of neuromasts. Growing lateral line axons are located superficially under the skin and can be labeled in living zebrafish using fluorescent protein expression. This system provides a relatively straightforward approach for in vivo time-lapse imaging of neuronal development in an undergraduate setting. Here we describe an upper-level neurobiology laboratory module in which students investigate aspects of axonal development in the zebrafish lateral line system. Students learn to handle and image living fish, collect time-lapse videos of moving mitochondria, and quantitatively measure mitochondrial dynamics by generating and analyzing kymographs of their movements. Energy demands may differ between axons with extending growth cones versus axons that have already reached their targets and are forming synapses. Since relatively little is known about this process in developing lateral line axons, students generate and test their own hypotheses regarding how mitochondrial dynamics may differ at two different time points in axonal development. Students also learn to incorporate into their analysis a powerful yet accessible quantitative tool, the kymograph, which is used to graph movement over time. After students measure and quantify dynamics in living fish at 1 and 2 days post fertilization, this module extends into independent projects, in which students can expand their studies in a number of different, inquiry-driven directions. The project can also be pared down for courses that wish to focus solely on the quantitative analysis (without fish handling), or vice versa. This research module provides a useful approach for the design of open-ended laboratory research projects that integrate the scientific process into undergraduate Biology courses, as encouraged by the AAAS and NSF Vision and Change Initiative.

Application of image processing to calculate the number of fish seeds using raspberry-pi

NASA Astrophysics Data System (ADS)

Rahmadiansah, A.; Kusumawardhani, A.; Duanto, F. N.; Qoonita, F.

2018-03-01

Many fish cultivator in Indonesia who suffered losses due to the sale and purchase of fish seeds did not match the agreed amount. The loss is due to the calculation of fish seed still using manual method. To overcome these problems, then in this study designed fish counting system automatically and real-time fish using the image processing based on Raspberry Pi. Used image processing because it can calculate moving objects and eliminate noise. Image processing method used to calculate moving object is virtual loop detector or virtual detector method and the approach used is “double difference image”. The “double difference” approach uses information from the previous frame and the next frame to estimate the shape and position of the object. Using these methods and approaches, the results obtained were quite good with an average error of 1.0% for 300 individuals in a test with a virtual detector width of 96 pixels and a slope of 1 degree test plane.

Improved exploration of fishery resources through the integration of remotely sensed merged sea level anomaly, chlorophyll concentration, and sea surface temperature

NASA Astrophysics Data System (ADS)

Priya, R. Kanmani Shanmuga; Balaguru, B.; Ramakrishnan, S.

2013-10-01

The capabilities of evolving satellite remote sensing technology, combined with conventional data collection techniques, provide a powerful tool for efficient and cost effective management of living marine resources. Fishes are the valuable living marine resources producing food, profit and pleasure to the human community. Variations in oceanic condition play a role in natural fluctuations of fish stocks. The Satellite Altimeter derived Merged Sea Level Anomaly(MSLA) results in the better understanding of ocean variability and mesosclae oceanography and provides good possibility to reveal the zones of high dynamic activity. This study comprised the synergistic analysis of signatures of SEAWIFS derived chlorophyll concentration, National Oceanic and Atmospheric Administration-Advanced Very High Resolution Radiometer(NOAA-AVHRR) derived Sea Surface Temperature and the monthly Merged Sea Level Anomaly data derived from Topex/Poseidon, Jason-1 and ERS-1 Altimeters for the past 7 years during the period from 1998 to 2004. The overlapping Chlorophyll, SST and MSLA were suggested for delineating Potential Fishing Zones (PFZs). The Chlorophyll and SST data set were found to have influenced by short term persistence from days to week while MSLA signatures of respective features persisted for longer duration. Hence, the study used Altimeter derived MSLA as an index for long term variability detection of fish catches along with Chlorophyll and SST images and the maps showing PFZs of the study area were generated. The real time Fishing statistics of the same duration were procured from FSI Mumbai. The catch contours were generated with respect to peak spectra of chlorophyll variation and trough spectra of MSLA and SST variation. The vice- a- versa patterns were observed in the poor catch contours. The Catch Per Unit Effort (CPUE) for each fishing trail was calculated to normalize the fish catch. Based on the statistical analysis the actual CPUEs were classified at each probable MSLA depth zones and plotted on the same images.

Quantifying fish swimming behavior in response to acute exposure of aqueous copper using computer assisted video and digital image analysis

USGS Publications Warehouse

Calfee, Robin D.; Puglis, Holly J.; Little, Edward E.; Brumbaugh, William G.; Mebane, Christopher A.

2016-01-01

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors.

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis

PubMed Central

Calfee, Robin D.; Puglis, Holly J.; Little, Edward E.; Brumbaugh, William G.; Mebane, Christopher A.

2016-01-01

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors. PMID:26967350

A low-cost drone based application for identifying and mapping of coastal fish nursery grounds

NASA Astrophysics Data System (ADS)

Ventura, Daniele; Bruno, Michele; Jona Lasinio, Giovanna; Belluscio, Andrea; Ardizzone, Giandomenico

2016-03-01

Acquiring seabed, landform or other topographic data in the field of marine ecology has a pivotal role in defining and mapping key marine habitats. However, accessibility for this kind of data with a high level of detail for very shallow and inaccessible marine habitats has been often challenging, time consuming. Spatial and temporal coverage often has to be compromised to make more cost effective the monitoring routine. Nowadays, emerging technologies, can overcome many of these constraints. Here we describe a recent development in remote sensing based on a small unmanned drone (UAVs) that produce very fine scale maps of fish nursery areas. This technology is simple to use, inexpensive, and timely in producing aerial photographs of marine areas. Both technical details regarding aerial photos acquisition (drone and camera settings) and post processing workflow (3D model generation with Structure From Motion algorithm and photo-stitching) are given. Finally by applying modern algorithm of semi-automatic image analysis and classification (Maximum Likelihood, ECHO and Object-based Image Analysis) we compared the results of three thematic maps of nursery area for juvenile sparid fishes, highlighting the potential of this method in mapping and monitoring coastal marine habitats.

Signal amplification of FISH for automated detection using image cytometry.

PubMed

Truong, K; Boenders, J; Maciorowski, Z; Vielh, P; Dutrillaux, B; Malfoy, B; Bourgeois, C A

1997-05-01

The purpose of this study was to improve the detection of FISH signals, in order that spot counting by a fully automated image cytometer be comparable to that obtained visually under the microscope. Two systems of spot scoring, visual and automated counting, were investigated in parallel on stimulated human lymphocytes with FISH using a biotinylated centromeric probe for chromosome 3. Signal characteristics were first analyzed on images recorded with a coupled charge device (CCD) camera. Number of spots per nucleus were scored visually on these recorded images versus automatically with a DISCOVERY image analyzer. Several fluochromes, amplification and pretreatments were tested. Our results for both visual and automated scoring show that the tyramide amplification system (TSA) gives the best amplification of signal if pepsin treatment is applied prior to FISH. Accuracy of the automated scoring, however, remained low (58% of nuclei containing two spots) compared to the visual scoring because of the high intranuclear variation between FISH spots.

Reflective Light Modulation by Cephalopods in Shallow Nearshore Habitats

DTIC Science & Technology

2008-01-01

changeable camouflage patterns known in biology. Fish and insects are studied comparatively. APPROACH High-resolution digital still images (Canon EOS 1Ds...quantified in the digital images. HDTV video is used to follow foraging cephalopods and fish to document (a) speed of body patterning changes and (b...images of cephalopods and fishes . Briefly, the breakdown is as follows. (1) Izmir, Turkey, March 2008, to photograph the common European cuttlefish

Detection and recognition of uneaten fish food pellets in aquaculture using image processing

NASA Astrophysics Data System (ADS)

Liu, Huanyu; Xu, Lihong; Li, Dawei

2015-03-01

The waste of fish food has always been a serious problem in aquaculture. On one hand, the leftover fish food spawns a big waste in the aquaculture industry because fish food accounts for a large proportion of the investment. On the other hand, the left over fish food may pollute the water and make fishes sick. In general, the reason for fish food waste is that there is no feedback about the consumption of delivered fish food after feeding. So it is extremely difficult for fish farmers to determine the amount of feedstuff that should be delivered each time and the feeding intervals. In this paper, we propose an effective method using image processing techniques to solve this problem. During feeding events, we use an underwater camera with supplementary LED lights to obtain images of uneaten fish food pellets on the tank bottom. An algorithm is then developed to figure out the number of left pellets using adaptive Otsu thresholding and a linear-time component labeling algorithm. This proposed algorithm proves to be effective in handling the non-uniform lighting and very accurate number of pellets are counted in experiments.

Fish Karyome: A karyological information network database of Indian Fishes.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

2012-01-01

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

The Relevance of External Quality Assessment for Molecular Testing for ALK Positive Non-Small Cell Lung Cancer: Results from Two Pilot Rounds Show Room for Optimization

PubMed Central

Tembuyser, Lien; Tack, Véronique; Zwaenepoel, Karen; Pauwels, Patrick; Miller, Keith; Bubendorf, Lukas; Kerr, Keith; Schuuring, Ed; Thunnissen, Erik; Dequeker, Elisabeth M. C.

2014-01-01

Background and Purpose Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK rearrangement status is a critical biomarker to predict response to tyrosine kinase inhibitors such as crizotinib. To promote high quality testing in non-small cell lung cancer, the European Society of Pathology has introduced an external quality assessment scheme. This article summarizes the results of the first two pilot rounds organized in 2012–2013. Materials and Methods Tissue microarray slides consisting of cell-lines and resection specimens were distributed with the request for routine ALK testing using IHC or FISH. Participation in ALK FISH testing included the interpretation of four digital FISH images. Results Data from 173 different laboratories was obtained. Results demonstrate decreased error rates in the second round for both ALK FISH and ALK IHC, although the error rates were still high and the need for external quality assessment in laboratories performing ALK testing is evident. Error rates obtained by FISH were lower than by IHC. The lowest error rates were observed for the interpretation of digital FISH images. Conclusion There was a large variety in FISH enumeration practices. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing. PMID:25386659

The relevance of external quality assessment for molecular testing for ALK positive non-small cell lung cancer: results from two pilot rounds show room for optimization.

PubMed

Tembuyser, Lien; Tack, Véronique; Zwaenepoel, Karen; Pauwels, Patrick; Miller, Keith; Bubendorf, Lukas; Kerr, Keith; Schuuring, Ed; Thunnissen, Erik; Dequeker, Elisabeth M C

2014-01-01

Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK rearrangement status is a critical biomarker to predict response to tyrosine kinase inhibitors such as crizotinib. To promote high quality testing in non-small cell lung cancer, the European Society of Pathology has introduced an external quality assessment scheme. This article summarizes the results of the first two pilot rounds organized in 2012-2013. Tissue microarray slides consisting of cell-lines and resection specimens were distributed with the request for routine ALK testing using IHC or FISH. Participation in ALK FISH testing included the interpretation of four digital FISH images. Data from 173 different laboratories was obtained. Results demonstrate decreased error rates in the second round for both ALK FISH and ALK IHC, although the error rates were still high and the need for external quality assessment in laboratories performing ALK testing is evident. Error rates obtained by FISH were lower than by IHC. The lowest error rates were observed for the interpretation of digital FISH images. There was a large variety in FISH enumeration practices. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing.

Automated Image Analysis of HER2 Fluorescence In Situ Hybridization to Refine Definitions of Genetic Heterogeneity in Breast Cancer Tissue

PubMed Central

Radziuviene, Gedmante; Rasmusson, Allan; Augulis, Renaldas; Lesciute-Krilaviciene, Daiva; Laurinaviciene, Aida; Clim, Eduard

2017-01-01

Human epidermal growth factor receptor 2 gene- (HER2-) targeted therapy for breast cancer relies primarily on HER2 overexpression established by immunohistochemistry (IHC) with borderline cases being further tested for amplification by fluorescence in situ hybridization (FISH). Manual interpretation of HER2 FISH is based on a limited number of cells and rather complex definitions of equivocal, polysomic, and genetically heterogeneous (GH) cases. Image analysis (IA) can extract high-capacity data and potentially improve HER2 testing in borderline cases. We investigated statistically derived indicators of HER2 heterogeneity in HER2 FISH data obtained by automated IA of 50 IHC borderline (2+) cases of invasive ductal breast carcinoma. Overall, IA significantly underestimated the conventional HER2, CEP17 counts, and HER2/CEP17 ratio; however, it collected more amplified cells in some cases below the lower limit of GH definition by manual procedure. Indicators for amplification, polysomy, and bimodality were extracted by factor analysis and allowed clustering of the tumors into amplified, nonamplified, and equivocal/polysomy categories. The bimodality indicator provided independent cell diversity characteristics for all clusters. Tumors classified as bimodal only partially coincided with the conventional GH heterogeneity category. We conclude that automated high-capacity nonselective tumor cell assay can generate evidence-based HER2 intratumor heterogeneity indicators to refine GH definitions. PMID:28752092

Automated Image Analysis of HER2 Fluorescence In Situ Hybridization to Refine Definitions of Genetic Heterogeneity in Breast Cancer Tissue.

PubMed

Radziuviene, Gedmante; Rasmusson, Allan; Augulis, Renaldas; Lesciute-Krilaviciene, Daiva; Laurinaviciene, Aida; Clim, Eduard; Laurinavicius, Arvydas

2017-01-01

Human epidermal growth factor receptor 2 gene- (HER2-) targeted therapy for breast cancer relies primarily on HER2 overexpression established by immunohistochemistry (IHC) with borderline cases being further tested for amplification by fluorescence in situ hybridization (FISH). Manual interpretation of HER2 FISH is based on a limited number of cells and rather complex definitions of equivocal, polysomic, and genetically heterogeneous (GH) cases. Image analysis (IA) can extract high-capacity data and potentially improve HER2 testing in borderline cases. We investigated statistically derived indicators of HER2 heterogeneity in HER2 FISH data obtained by automated IA of 50 IHC borderline (2+) cases of invasive ductal breast carcinoma. Overall, IA significantly underestimated the conventional HER2, CEP17 counts, and HER2/CEP17 ratio; however, it collected more amplified cells in some cases below the lower limit of GH definition by manual procedure. Indicators for amplification, polysomy, and bimodality were extracted by factor analysis and allowed clustering of the tumors into amplified, nonamplified, and equivocal/polysomy categories. The bimodality indicator provided independent cell diversity characteristics for all clusters. Tumors classified as bimodal only partially coincided with the conventional GH heterogeneity category. We conclude that automated high-capacity nonselective tumor cell assay can generate evidence-based HER2 intratumor heterogeneity indicators to refine GH definitions.

Methylation pattern of fish lymphocystis disease virus DNA.

PubMed Central

Wagner, H; Simon, D; Werner, E; Gelderblom, H; Darai, C; Flügel, R M

1985-01-01

The content and distribution of 5-methylcytosine in DNA from fish lymphocystis disease virus was analyzed by high-pressure liquid chromatography, nearest-neighbor analysis, and with restriction endonucleases. We found that 22% of all C residues were methylated, including methylation of the following dinucleotide sequences: CpG to 75%, CpC to ca. 1%, and CpA to 2 to 5%. Comparison of relative digestion of viral DNA with MspI and HpaII indicated that CCGG sequences were almost completely methylated at the inner C. The degree of methylation of GCGC was much lower. The methylation pattern of fish lymphocystis disease virus DNA differed from that of the host cell DNA. Images PMID:3973962

3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines.

PubMed

Kocanova, Silvia; Goiffon, Isabelle; Bystricky, Kerstin

2018-06-01

Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines. Copyright © 2018 Elsevier Inc. All rights reserved.

Fish freshness estimation using eye image processing under white and UV lightings

NASA Astrophysics Data System (ADS)

Kanamori, Katsuhiro; Shirataki, Yuri; Liao, Qiuhong; Ogawa, Yuichi; Suzuki, Tetsuhito; Kondo, Naoshi

2017-05-01

A non-destructive method of estimating the freshness of fish is required for appropriate price setting and food safety. In particular, for determining the possibility of eating raw fish (sashimi), freshness estimation is critical. We studied such an estimation method by capturing images of fish eyes and performing image processing using the temporal changes of the luminance of pupil and iris. To detect subtle non-visible changes of these features, we used UV (375 nm) light illumination in addition to visible white light illumination. Polarization and two-channel LED techniques were used to remove strong specular reflection from the cornea of the eye and from clear-plastic wrap used to cover the fish to maintain humidity. Pupil and iris regions were automatically detected separately by image processing after the specular reflection removal process, and two types of eye contrast were defined as the ratio of mean and median pixel values of each region. Experiments using 16 Japanese dace (Tribolodon hakonensis) at 23° and 85% humidity for 24 hours were performed. The eye contrast of raw fish increase non-linearly in the initial period and then decreased; however, that of frozen-thawed fish decreased linearly throughout 24 hours, regardless of the lighting. Interestingly, the eye contrast using UV light showed a higher correlation with time than that using white light only in the case of raw fish within the early 6- hour period postmortem. These results show the possibility of estimating fish freshness in the initial stage when fish are eaten raw using white and UV lightings.

Impact and fracture analysis of fish scales from Arapaima gigas.

PubMed

Torres, F G; Malásquez, M; Troncoso, O P

2015-06-01

Fish scales from the Amazonian fish Arapaima gigas have been characterised to study their impact and fracture behaviour at three different environmental conditions. Scales were cut in two different directions to analyse the influence of the orientation of collagen layers. The energy absorbed during impact tests was measured for each sample and SEM images were taken after each test in order to analyse the failure mechanisms. The results showed that scales tested at cryogenic temperatures display fragile behaviour, while scales tested at room temperature did not fracture. Different failure mechanisms have been identified, analysed and compared with the failure modes that occur in bone. The impact energy obtained for fish scales was two to three times higher than the values reported for bone in the literature. Copyright © 2015 Elsevier B.V. All rights reserved.

In vivo cell tracking and quantification method in adult zebrafish

NASA Astrophysics Data System (ADS)

Zhang, Li; Alt, Clemens; Li, Pulin; White, Richard M.; Zon, Leonard I.; Wei, Xunbin; Lin, Charles P.

2012-03-01

Zebrafish have become a powerful vertebrate model organism for drug discovery, cancer and stem cell research. A recently developed transparent adult zebrafish using double pigmentation mutant, called casper, provide unparalleled imaging power in in vivo longitudinal analysis of biological processes at an anatomic resolution not readily achievable in murine or other systems. In this paper we introduce an optical method for simultaneous visualization and cell quantification, which combines the laser scanning confocal microscopy (LSCM) and the in vivo flow cytometry (IVFC). The system is designed specifically for non-invasive tracking of both stationary and circulating cells in adult zebrafish casper, under physiological conditions in the same fish over time. The confocal imaging part in this system serves the dual purposes of imaging fish tissue microstructure and a 3D navigation tool to locate a suitable vessel for circulating cell counting. The multi-color, multi-channel instrument allows the detection of multiple cell populations or different tissues or organs simultaneously. We demonstrate initial testing of this novel instrument by imaging vasculature and tracking circulating cells in CD41: GFP/Gata1: DsRed transgenic casper fish whose thrombocytes/erythrocytes express the green and red fluorescent proteins. Circulating fluorescent cell incidents were recorded and counted repeatedly over time and in different types of vessels. Great application opportunities in cancer and stem cell researches are discussed.

Identification of Potential Fishing Grounds Using Geospatial Technique

NASA Astrophysics Data System (ADS)

Abdullah, Muhammad

2016-07-01

Fishery resources surveys using actual sampling and data collection methods require extensive ship time and sampling time. Informative data from satellite plays a vital role in fisheries application. Satellite Remote Sensing techniques can be used to detect fish aggregation just like visual fish identification ultimately these techniques can be used to predict the potential fishing zones by measuring the parameters which affect the distribution of fishes. Remote sensing is a time saving technique to locate fishery resources along the coast. Pakistan has a continental shelf area of 50,270 km2 and coastline length of 1,120 km. The total maritime zone of Pakistan is over 30 percent of the land area. Fishery plays an important role in the national economy. The marine fisheries sector is the main component, contributing about 57 percent in terms of production. Fishery is the most important economic activity in the villages and towns along the coast, and in most of the coastal villages and settlements it is the sole source of employment and income generation. Fishing by fishermen is done on the sole basis of repeated experiments and collection of information from other fishermen. Often they are in doubt about the location of potential fishing zones. This leads to waste of time and money, adversely affecting fishermen incomes and over or under-exploitation of fishing zones. The main purpose of this study was to map potential fishing grounds by identifying various environmental parameters which impact fish aggregation along the Pakistan coastline. The primary reason of this study is the fact that the fishing communities of Pakistan's coastal regions are extremely poor and lack knowledge of the modern tools and techniques that may be incorporated to enhance their yield and thus, improve their livelihood. Using geospatial techniques in order to accurately map the potential fishing zones based on sea surface temperature (SST) and chlorophyll -a content, in conjunction with active use of GPS navigation systems can go a long way in improving the output of the fishing community. For this study, satellite data of sea surface temperature and chlorophyll-a content product of MODIS aqua 250 meters, 8 day composite was used. Secondary field survey of Fish and Agriculture Organization (FAO) in month of October was used to assist the fish catch, SST and Chlorophyll-a concentration in Exclusive economic zone (EEZ) of Pakistan, The next step was to establish a GIS database of fish catch data along with the geographical coordinates of the catch spot. After that MODIS SST and Chlorophyll-a concentration image of October 2010 was acquired, the product was converted to tiff format and projection applied for further processing. SST and chlorophyll-a images were reclassified using reclassification technique and then SST and chlorophyll-a values were extracted which were then used to overlay on fish catch data to extract best catch. GIS techniques such as suitability analysis was performed which helped to identify the potential fishing zones in the study area. The next step was to acquire local fishermen knowledge by using questionnaires to verify the sites identified for their fish catch potential, after verification the methodology was applied on whole year (2010) comprising of 45 images of MODIS sensor. Final potential fishing grounds maps were generated using satellite and in-situ measurements. Once we accurately identify the fishing areas with a high catch potential, it may be possible to estimate the overall fishing resources of the study area. This study will be an outline for local fisherman and marine fisheries department this will help them to monitor real time mapping of fish aggregation in Pakistan EEZ. Fish is important for food industries and national economy. Thus this study can facilitate the government, investors and stakeholders to design export policies that can eventually help the country economically while not depleting the marine resources. Remotely sensed data can therefore prove to be an economical and time saving method of carrying out analysis for maritime fishing activities. Such studies, if used intelligently can help assure food security to the nation and promote Pakistan's coastal resources in world market.

Hematological findings in neotropical fish Hoplias malabaricus exposed to subchronic and dietary doses of methylmercury, inorganic lead, and tributyltin chloride.

PubMed

Oliveira Ribeiro, C A; Filipak Neto, F; Mela, M; Silva, P H; Randi, M A F; Rabitto, I S; Alves Costa, J R M; Pelletier, E

2006-05-01

Hematological indices are gaining general acceptance as valuable tools in monitoring various aspects the health of fish exposed to contaminants. In this work some effects of methyl mercury (MeHg), inorganic lead (Pb2+), and tributyltin (TBT) in a tropical fish species were evaluated by hematological methods after a trophic exposition at a subchronic level. Forty-two mature individuals of the freshwater top predator fish Hoplias malabaricus were exposed to trophic doses (each 5 days) of MeHg (0.075 microg g(-1)), Pb2+ (21 microg g(-1)), and TBT (0.3 microg g(-1)) using young fish Astyanax sp. as prey vehicle. After 14 successive doses over 70 days, blood was sampled from exposed and control groups to evaluate hematological effects of metals on erythrocytes, total leukocytes and differential leukocytes counts, hematocrit, hemoglobin concentration, and red blood cell indices mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC). Transmission electron microscopy and image analysis of erythrocytes were also used to investigate some morphometric parameters. Results show no significant effects in MCH and MCHC for all tested metals, but differences were found in erythrocytes, hemoglobin, hematocrit, MCV, and white blood cells counts. The number of leukocytes was increased in the presence of MeHg, suggesting effects on the immune system. Also the MCV increased in individuals exposed to MeHg. No ultrastructural damages were observed in red blood cells but the image analysis using light microscopy revealed differences in area, elongation, and roundness of erythrocytes from individuals exposed to Pb2+ and TBT but not in the group exposed to MeHg. The present work shows that changes in hematological and blood indices could highlight some barely detectable metal effects in fish after laboratory exposure to contaminated food, but their application in field biomonitoring using H. malabaricus will need more detailed studies and a careful consideration of environmental parameters.

Fish skin provides invisibility in open ocean (image 11)

NSF Multimedia

2017-02-10

Skin preparation from fish shows birefringence under cross polarization microscopy Skin preparation from fish shows birefringence under cross polarization microscopySkin preparation from fish shows birefringence under cross polarization microscopy Skin pr

Acoustic Imaging Evaluation of Juvenile Salmonid Behavior in the Immediate Forebay of the Water Temperature Control Tower at Cougar Dam, 2010

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, Fenton; Johnson, Gary E.; Royer, Ida M.

This report presents the results of an evaluation of juvenile Chinook salmon (Oncorhynchus tshawytscha) behavior at Cougar Dam on the south fork of the McKenzie River in Oregon in 2010. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers (USACE). The overall goal of the study was to characterize juvenile salmonid behavior and movement patterns in the immediate forebay of the Water Temperature Control (WTC) tower of the dam for USACE and fisheries resource managers use in making decisions about bioengineering designs for long-term structures and/or operations to facilitate safe downstream passagemore » for juvenile salmonids. We collected acoustic imaging (Dual-Frequency Identification Sonar; DIDSON) data from March 1, 2010, through January 31, 2011. Juvenile salmonids (hereafter, called 'fish') were present in the immediate forebay of the WTC tower throughout the study. Fish abundance index was low in early spring (<200 fish per sample-day), increased in late April, and peaked on May 19 (6,039 fish). A second peak was observed on June 6 (2904 fish). Fish abundance index decreased in early June and remained low in the summer months (<100 fish per sample-day). During the fall and winter, fish numbers varied with a peak on November 10 (1881 fish) and a minimum on December 7 (12 fish). A second, smaller, peak occurred on December 22 (607 fish). A univariate statistical analysis indicated fish abundance index (log10-transformed) was significantly (P<0.05) positively correlated with forebay elevation, velocity over the WTC tower intake gate weirs, and river flows into the reservoir. A subsequent multiple regression analysis resulted in a model (R2=0.70) predicting fish abundance (log-transformed index values) using two independent variables of mean forebay elevation and the log10 of the forebay elevation range. From the approximate fish length measurements made using the DIDSON imaging software, the average fish length during early spring 2010 was 214 {+-} 86 mm (standard deviation). From May through early November, the average fish length remained relatively consistent (132 {+-} 54 mm), after which average lengths increased to 295 {+-} 148 mm for mid-November though early December. From mid-December through January the average fish length decreased to 151 {+-} 76 mm. Milling in front of the WTC tower was the most common fish behavior observed throughout the study period. Traversing along the front of the tower, east-to-west and west-to-east, was the next common behavior. The percentage of fish events showing movement from the forebay to the tower or from the tower to the forebay was generally low throughout the spring, summer, and early fall (0 to 30% for both directions combined, March through early November). From mid-November 2010 through the end of the study (January 31, 2011), the combined percentages of fish moving into and out of the tower were higher (25 to 70%) than during previous months of the study. Schooling behavior was most distinct in the spring. Schooling events were present in 30 to 96% of the fish events during that period, with a peak on May 19. Schooling events were also present in the summer, but at lower numbers. With the exception of some schooling in mid-December, few to no schooling events were observed in the fall and winter months. Diel distributions for schooling fish during spring and fall months indicate schooling was concentrated during daylight hours and no schooling was observed at night. However, in December, schooling occurred at night, after midnight, and during daylight hours. Predator activity, most likely bull trout or rainbow trout according to a USACE biologist, was observed during late spring, when fish abundance index and schooling were highest for the year, and again in the fall months when fish events increased from a summer low. No predator activity was observed in the summer, and little activity occurred during the winter months.« less

Extraction and characterization of gelatin biopolymer from black tilapia (Oreochromis mossambicus) scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sockalingam, K., E-mail: gd130106@siswa.uthm.edu.my; Abdullah, H. Z., E-mail: hasan@uthm.edu.my

2015-07-22

Black tilapia (Oreochromis mossambicus) fish wastes (scales) were evaluated for its suitability as sources of gelatin. Scales were subjected to acid treatment for demineralization before it undergoes thermal extraction process. The raw scales were characterized via Scanning Electron Microscopy (SEM), which demarcated the cycloid pattern of the scales. SEM images also reveal the presence of collagen fiber in the fish scale. The black tilapia fish scales yields 11.88 % of gelatin, indicating the possibility of this fish species as sources of gelatin. Further characterizations were done on both raw scale and extracted gelatin through Fourier Transform Infrared Spectroscopy (FTIR) andmore » proximate analysis. The scale gelatin shows high protein content (86.9 %) with low moisture (8.2 %) and ash (1.4 %). This further proves the effectiveness of the demineralization and extraction method used. The black tilapia fish scale is found to be a prospective source of gelatin with good chemical and functional properties.« less

The Use of 3D Telomere FISH for the Characterization of the Nuclear Architecture in EBV-Positive Hodgkin's Lymphoma.

PubMed

Knecht, Hans; Mai, Sabine

2017-01-01

The 3D nuclear architecture is closely related to cellular functions and chromosomes are organized in distinct territories. Quantitative 3D telomere FISH analysis (3D Q-FISH) and 3D super-resolution imaging (3D-SIM) at a resolution up to 80 nm as well as the recently developed combined quantitative 3D TRF2-telomere immune FISH technique (3D TRF2/Telo-Q-FISH) have substantially contributed to elucidate molecular pathogenic mechanisms of hematological diseases. Here we report the methods we applied to uncover major molecular steps involved in the pathogenesis of EBV-associated Hodgkin's lymphoma. These methods allowed us to identify the EBV-encoded oncoprotein LMP1 as a key element in the formation of Hodgkin (H-cell) and multinucleated Reed-Sternberg cells (RS-cell), the diagnostic tumor cell of classical Hodgkin's lymphoma (cHL). LMP1 mediates multinuclearity through downregulation of shelterin proteins, in particular telomere repeat binding factor 2 (TRF2).

Analysis of image thresholding segmentation algorithms based on swarm intelligence

NASA Astrophysics Data System (ADS)

Zhang, Yi; Lu, Kai; Gao, Yinghui; Yang, Bo

2013-03-01

Swarm intelligence-based image thresholding segmentation algorithms are playing an important role in the research field of image segmentation. In this paper, we briefly introduce the theories of four existing image segmentation algorithms based on swarm intelligence including fish swarm algorithm, artificial bee colony, bacteria foraging algorithm and particle swarm optimization. Then some image benchmarks are tested in order to show the differences of the segmentation accuracy, time consumption, convergence and robustness for Salt & Pepper noise and Gaussian noise of these four algorithms. Through these comparisons, this paper gives qualitative analyses for the performance variance of the four algorithms. The conclusions in this paper would give a significant guide for the actual image segmentation.

Small Fish Species as Powerful Model Systems to Study Vertebrate Physiology in Space

NASA Astrophysics Data System (ADS)

Muller, M.; Aceto, J.; Dalcq, J.; Alestrom, P.; Nourizadeh-Lillabadi, R.; Goerlich, R.; Schiller, V.; Winkler, C.; Renn, J.; Eberius, M.; Slenzka, K.

2008-06-01

Small fish models, mainly zebrafish (Danio rerio) and medaka (Oryzias latipes), have been used for many years as powerful model systems for vertebrate developmental biology. Moreover, these species are increasingly recognized as valuable systems to study vertebrate physiology, pathology, pharmacology and toxicology, including in particular bone physiology. The biology of small fishes presents many advantages, such as transparency of the embryos, external and rapid development, small size and easy reproduction. Further characteristics are particularly useful for space research or for large scale screening approaches. Finally, many technologies for easily characterizing bones are available. Our objective is to investigate the changes induced by microgravity in small fish. By combining whole genome analysis (microarray, DNA methylation, chromatin modification) with live imaging of selected genes in transgenic animals, a comprehensive and integrated characterization of physiological changes in space could be gained, especially concerning bone physiology.

HiCTMap: Detection and analysis of chromosome territory structure and position by high-throughput imaging.

PubMed

Jowhar, Ziad; Gudla, Prabhakar R; Shachar, Sigal; Wangsa, Darawalee; Russ, Jill L; Pegoraro, Gianluca; Ried, Thomas; Raznahan, Armin; Misteli, Tom

2018-06-01

The spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells. HiCTMap is a high-throughput imaging-based chromosome detection method which enables routine analysis of chromosome structure and nuclear position. Using an optimized FISH staining protocol in a 384-well plate format in conjunction with a bespoke automated image analysis workflow, HiCTMap faithfully detects chromosome territories and their position in 2D and 3D in a large population of cells per experimental condition. We apply this novel technique to visualize chromosomes 18, X, and Y in male and female primary human skin fibroblasts, and show accurate detection of the correct number of chromosomes in the respective genotypes. Given the ability to visualize and quantitatively analyze large numbers of nuclei, we use HiCTMap to measure chromosome territory area and volume with high precision and determine the radial position of chromosome territories using either centroid or equidistant-shell analysis. The HiCTMap protocol is also compatible with RNA FISH as demonstrated by simultaneous labeling of X chromosomes and Xist RNA in female cells. We suggest HiCTMap will be a useful tool for routine precision mapping of chromosome territories in a wide range of cell types and tissues. Published by Elsevier Inc.

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Hybrid ANN optimized artificial fish swarm algorithm based classifier for classification of suspicious lesions in breast DCE-MRI

NASA Astrophysics Data System (ADS)

Janaki Sathya, D.; Geetha, K.

2017-12-01

Automatic mass or lesion classification systems are developed to aid in distinguishing between malignant and benign lesions present in the breast DCE-MR images, the systems need to improve both the sensitivity and specificity of DCE-MR image interpretation in order to be successful for clinical use. A new classifier (a set of features together with a classification method) based on artificial neural networks trained using artificial fish swarm optimization (AFSO) algorithm is proposed in this paper. The basic idea behind the proposed classifier is to use AFSO algorithm for searching the best combination of synaptic weights for the neural network. An optimal set of features based on the statistical textural features is presented. The investigational outcomes of the proposed suspicious lesion classifier algorithm therefore confirm that the resulting classifier performs better than other such classifiers reported in the literature. Therefore this classifier demonstrates that the improvement in both the sensitivity and specificity are possible through automated image analysis.

RNA Imaging with Multiplexed Error Robust Fluorescence in situ Hybridization

PubMed Central

Moffitt, Jeffrey R.; Zhuang, Xiaowei

2016-01-01

Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single-cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule Fluorescence In Situ Hybridization (smFISH)—an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context—provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here we describe Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves. PMID:27241748

Automated processing of zebrafish imaging data: a survey.

PubMed

Mikut, Ralf; Dickmeis, Thomas; Driever, Wolfgang; Geurts, Pierre; Hamprecht, Fred A; Kausler, Bernhard X; Ledesma-Carbayo, María J; Marée, Raphaël; Mikula, Karol; Pantazis, Periklis; Ronneberger, Olaf; Santos, Andres; Stotzka, Rainer; Strähle, Uwe; Peyriéras, Nadine

2013-09-01

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.

Automated Processing of Zebrafish Imaging Data: A Survey

PubMed Central

Dickmeis, Thomas; Driever, Wolfgang; Geurts, Pierre; Hamprecht, Fred A.; Kausler, Bernhard X.; Ledesma-Carbayo, María J.; Marée, Raphaël; Mikula, Karol; Pantazis, Periklis; Ronneberger, Olaf; Santos, Andres; Stotzka, Rainer; Strähle, Uwe; Peyriéras, Nadine

2013-01-01

Abstract Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines. PMID:23758125

Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization.

PubMed

Grigoryan, Artyom M; Dougherty, Edward R; Kononen, Juha; Bubendorf, Lukas; Hostetter, Galen; Kallioniemi, Olli

2002-01-01

Fluorescence in situ hybridization (FISH) is a molecular diagnostic technique in which a fluorescent labeled probe hybridizes to a target nucleotide sequence of deoxyribose nucleic acid. Upon excitation, each chromosome containing the target sequence produces a fluorescent signal (spot). Because fluorescent spot counting is tedious and often subjective, automated digital algorithms to count spots are desirable. New technology provides a stack of images on multiple focal planes throughout a tissue sample. Multiple-focal-plane imaging helps overcome the biases and imprecision inherent in single-focal-plane methods. This paper proposes an algorithm for global spot counting in stacked three-dimensional slice FISH images without the necessity of nuclei segmentation. It is designed to work in complex backgrounds, when there are agglomerated nuclei, and in the presence of illumination gradients. It is based on the morphological top-hat transform, which locates intensity spikes on irregular backgrounds. After finding signals in the slice images, the algorithm groups these together to form three-dimensional spots. Filters are employed to separate legitimate spots from fluorescent noise. The algorithm is set in a comprehensive toolbox that provides visualization and analytic facilities. It includes simulation software that allows examination of algorithm performance for various image and algorithm parameter settings, including signal size, signal density, and the number of slices.

Whales and waves: Humpback whale foraging response and the shoaling of internal waves at Stellwagen Bank

NASA Astrophysics Data System (ADS)

Pineda, Jesús; Starczak, Victoria; da Silva, José C. B.; Helfrich, Karl; Thompson, Michael; Wiley, David

2015-04-01

We tested the hypothesis that humpback whales aggregate at the southern flank of Stellwagen Bank (SB) in response to internal waves (IWs) generated semidiurnally at Race Point (RP) channel because of the presence of their preferred prey, planktivorous fish, which in turn respond to zooplankton concentrated by the predictable IWs. Analysis of synthetic aperture radar (SAR) images indicates that RP IWs approach the southern flank of SB frequently (˜62% of the images). Published reports of whale sighting data and archived SAR images point to a coarse spatial coincidence between whales and Race Point IWs at SB's southern flank. The responses of whales to IWs were evaluated via sightings and behavior of humpback whales, and IWs were observed in situ by acoustic backscatter and temperature measurements. Modeling of IWs complemented the observations, and results indicate a change of ˜0.4 m/s in current velocity, and ˜1.5 Pa in dynamic pressure near the bottom, which may be sufficient for bottom fish to detect the IWs. However, fish were rare in our acoustic observations, and fish response to the IWs could not be evaluated. RP IWs do not represent the leading edge of the internal tide, and they may have less mass-transport potential than typical coastal IWs. There was large interannual variability in whale sightings at SB's southern flank, with decreases in both numbers of sightings and proportion of sightings where feeding was observed from 2008 to 2013. Coincidence of whales and IWs was inconsistent, and results do not support the hypothesis.

Developing national on-line services to annotate and analyse underwater imagery in a research cloud

NASA Astrophysics Data System (ADS)

Proctor, R.; Langlois, T.; Friedman, A.; Davey, B.

2017-12-01

Fish image annotation data is currently collected by various research, management and academic institutions globally (+100,000's hours of deployments) with varying degrees of standardisation and limited formal collaboration or data synthesis. We present a case study of how national on-line services, developed within a domain-oriented research cloud, have been used to annotate habitat images and synthesise fish annotation data sets collected using Autonomous Underwater Vehicles (AUVs) and baited remote underwater stereo-video (stereo-BRUV). Two developing software tools have been brought together in the marine science cloud to provide marine biologists with a powerful service for image annotation. SQUIDLE+ is an online platform designed for exploration, management and annotation of georeferenced images & video data. It provides a flexible annotation framework allowing users to work with their preferred annotation schemes. We have used SQUIDLE+ to sample the habitat composition and complexity of images of the benthos collected using stereo-BRUV. GlobalArchive is designed to be a centralised repository of aquatic ecological survey data with design principles including ease of use, secure user access, flexible data import, and the collection of any sampling and image analysis information. To easily share and synthesise data we have implemented data sharing protocols, including Open Data and synthesis Collaborations, and a spatial map to explore global datasets and filter to create a synthesis. These tools in the science cloud, together with a virtual desktop analysis suite offering python and R environments offer an unprecedented capability to deliver marine biodiversity information of value to marine managers and scientists alike.

Smart phone: a popular device supports amylase activity assay in fisheries research.

PubMed

Thongprajukaew, Karun; Choodum, Aree; Sa-E, Barunee; Hayee, Ummah

2014-11-15

Colourimetric determinations of amylase activity were developed based on a standard dinitrosalicylic acid (DNS) staining method, using maltose as the analyte. Intensities and absorbances of red, green and blue (RGB) were obtained with iPhone imaging and Adobe Photoshop image analysis. Correlation of green and analyte concentrations was highly significant, and the accuracy of the developed method was excellent in analytical performance. The common iPhone has sufficient imaging ability for accurate quantification of maltose concentrations. Detection limits, sensitivity and linearity were comparable to a spectrophotometric method, but provided better inter-day precision. In quantifying amylase specific activity from a commercial source (P>0.02) and fish samples (P>0.05), differences compared with spectrophotometric measurements were not significant. We have demonstrated that iPhone imaging with image analysis in Adobe Photoshop has potential for field and laboratory studies of amylase. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Identification of Hunger Behaviour of Lates Calcarifer through the Integration of Image Processing Technique and Support Vector Machine

NASA Astrophysics Data System (ADS)

Taha, Z.; Razman, M. A. M.; Adnan, F. A.; Ghani, A. S. Abdul; Majeed, A. P. P. Abdul; Musa, R. M.; Sallehudin, M. F.; Mukai, Y.

2018-03-01

Fish Hunger behaviour is one of the important element in determining the fish feeding routine, especially for farmed fishes. Inaccurate feeding routines (under-feeding or over-feeding) lead the fishes to die and thus, reduces the total production of fishes. The excessive food which is not eaten by fish will be dissolved in the water and thus, reduce the water quality (oxygen quantity in the water will be reduced). The reduction of oxygen (water quality) leads the fish to die and in some cases, may lead to fish diseases. This study correlates Barramundi fish-school behaviour with hunger condition through the hybrid data integration of image processing technique. The behaviour is clustered with respect to the position of the centre of gravity of the school of fish prior feeding, during feeding and after feeding. The clustered fish behaviour is then classified by means of a machine learning technique namely Support vector machine (SVM). It has been shown from the study that the Fine Gaussian variation of SVM is able to provide a reasonably accurate classification of fish feeding behaviour with a classification accuracy of 79.7%. The proposed integration technique may increase the usefulness of the captured data and thus better differentiates the various behaviour of farmed fishes.

A simple protocol for attenuating the auto-fluorescence of cyanobacteria for optimized fluorescence in situ hybridization (FISH) imaging.

PubMed

Zeller, Perrine; Ploux, Olivier; Méjean, Annick

2016-03-01

Cyanobacteria contain pigments, which generate auto-fluorescence that interferes with fluorescence in situ hybridization (FISH) imaging of cyanobacteria. We describe simple chemical treatments using CuSO4 or H2O2 that significantly reduce the auto-fluorescence of Microcystis strains. These protocols were successfully applied in FISH experiments using 16S rRNA specific probes and filamentous cyanobacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

Hematological findings in neotropical fish Hoplias malabaricus exposed to subchronic and dietary doses of methylmercury, inorganic lead, and tributyltin chloride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira Ribeiro, C.A.; Filipak Neto, F.; Mela, M.

2006-05-15

Hematological indices are gaining general acceptance as valuable tools in monitoring various aspects the health of fish exposed to contaminants. In this work some effects of methyl mercury (MeHg), inorganic lead (Pb{sup 2+}), and tributyltin (TBT) in a tropical fish species were evaluated by hematological methods after a trophic exposition at a subchronic level. Forty-two mature individuals of the freshwater top predator fish Hoplias malabaricus were exposed to trophic doses (each 5 days) of MeHg (0.075 {mu}g g{sup -1}), Pb{sup 2+} (21 {mu}g g{sup -1}), and TBT (0.3 {mu}g g{sup -1}) using young fish Astyanax sp. as prey vehicle. Aftermore » 14 successive doses over 70 days, blood was sampled from exposed and control groups to evaluate hematological effects of metals on erythrocytes, total leukocytes and differential leukocytes counts, hematocrit, hemoglobin concentration, and red blood cell indices mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC). Transmission electron microscopy and image analysis of erythrocytes were also used to investigate some morphometric parameters. Results show no significant effects in MCH and MCHC for all tested metals, but differences were found in erythrocytes, hemoglobin, hematocrit, MCV, and white blood cells counts. The number of leukocytes was increased in the presence of MeHg, suggesting effects on the immune system. Also the MCV increased in individuals exposed to MeHg. No ultrastructural damages were observed in red blood cells but the image analysis using light microscopy revealed differences in area, elongation, and roundness of erythrocytes from individuals exposed to Pb{sup 2+} and TBT but not in the group exposed to MeHg. The present work shows that changes in hematological and blood indices could highlight some barely detectable metal effects in fish after laboratory exposure to contaminated food, but their application in field biomonitoring using H. malabaricus will need more detailed studies and a careful consideration of environmental parameters.« less

Techno-Economic analysis of solar photovoltaic power plant for small scale fish processing in Kota Langsa - a case study

NASA Astrophysics Data System (ADS)

Widodo, S. B.; Hamdani; Rizal, T. A.; Pambudi, N. A.

2018-02-01

In Langsa, fisheries are the sector leaders by fulfilling a capacity of about 6,050 tons per year and on the other hand, fish-aquaculture reaches 1,200 tons per year on average. The fish processing is conducted through catches and aquaculture. The facilities on which this processing takes place are divided into an ice factory unit, a gutting and cutting unit, a drying unit and a curing unit. However, the energy and electricity costs during the production process has become major constraint because of the increase in the fishermen’s production and income. In this study, the potential and cost-effectiveness of photovoltaic solar power plant to meet the energy demands of fish processing units have been analysed. The energy requirements of fish processing units have reached an estimate of 130 kW, while the proposed design of solar photovoltaic electricity generation is of 200 kW in an area of 0,75 hectares. In this analysis, given the closeness between the location of the processing units and the fish supply auctions, the assumption is made that the photovoltaic plants (OTR) were installed on the roof of the building as compared to the solar power plants (OTL) installed on the outside of the location. The results shows that the levelized cost of OTR instalation is IDR 1.115 per kWh, considering 25 years of plant life-span at 10% of discount rate, with a simple payback period of 13.2 years. OTL levelized energy, on the other hand, is at IDR 997.5 per kWh with a simple payback period of 9.6 years. Blood is an essential component of living creatures in the vascular space. For possible disease identification, it can be tested through a blood test, one of which can be seen from the form of red blood cells. The normal and abnormal morphology of the red blood cells of a patient is very helpful to doctors in detecting a disease. With the advancement of digital image processing technology can be used to identify normal and abnormal blood cells of a patient. This research used self-organizing map method to classify the normal and abnormal form of red blood cells in the digital image. The use of self-organizing map neural network method can be implemented to classify the normal and abnormal form of red blood cells in the input image with 93,78% accuracy testing.

Assigning sex and reproductive stage to adult Lake Sturgeon using ultrasonography and common morphological measurements

USGS Publications Warehouse

Chiotti, Justin A.; Boase, James C.; Hondorp, Darryl W.; Briggs, Andrew S.

2016-01-01

Sex determination of fish species is difficult to assess when sexual dimorphism and gametes are not apparent. For threatened and endangered fish species, noninvasive techniques are needed when determining sex to minimize stress and the potential for mortality. We evaluated the use of a portable ultrasound unit to determine sex of Lake Sturgeon Acipenser fulvescens in the field. Ultrasound images were collected from 9 yellow-egg (F2, F3), 32 black-egg (F4, F5), and 107 fully developed male (M2) Lake Sturgeon. Two readers accurately assigned sex to 88–96% of fish, but accuracy varied in relation to maturity stage. Black-egg females and fully developed males were correctly identified for 89–100% of the fish sampled, while these two readers identified yellow-egg females only 33% and 67% of the time. Time spent collecting images ranged between 2 and 3 min once the user was comfortable with operating procedures. Discriminant analysis revealed the total length : girth ratio was a strong predictor of sex and maturity, correctly classifying 81% of black-egg females and 97% of the fully developed males. However, yellow-egg females were incorrectly classified on all occasions. This study shows the utility of using ultrasonography and a total length : girth ratio for sex determination of Lake Sturgeon in later reproductive stages around the spawning season.

The classification of hunger behaviour of Lates Calcarifer through the integration of image processing technique and k-Nearest Neighbour learning algorithm

NASA Astrophysics Data System (ADS)

Taha, Z.; Razman, M. A. M.; Ghani, A. S. Abdul; Majeed, A. P. P. Abdul; Musa, R. M.; Adnan, F. A.; Sallehudin, M. F.; Mukai, Y.

2018-04-01

Fish Hunger behaviour is essential in determining the fish feeding routine, particularly for fish farmers. The inability to provide accurate feeding routines (under-feeding or over-feeding) may lead the death of the fish and consequently inhibits the quantity of the fish produced. Moreover, the excessive food that is not consumed by the fish will be dissolved in the water and accordingly reduce the water quality through the reduction of oxygen quantity. This problem also leads the death of the fish or even spur fish diseases. In the present study, a correlation of Barramundi fish-school behaviour with hunger condition through the hybrid data integration of image processing technique is established. The behaviour is clustered with respect to the position of the school size as well as the school density of the fish before feeding, during feeding and after feeding. The clustered fish behaviour is then classified through k-Nearest Neighbour (k-NN) learning algorithm. Three different variations of the algorithm namely cosine, cubic and weighted are assessed on its ability to classify the aforementioned fish hunger behaviour. It was found from the study that the weighted k-NN variation provides the best classification with an accuracy of 86.5%. Therefore, it could be concluded that the proposed integration technique may assist fish farmers in ascertaining fish feeding routine.

A Featured-Based Strategy for Stereovision Matching in Sensors with Fish-Eye Lenses for Forest Environments

PubMed Central

Herrera, Pedro Javier; Pajares, Gonzalo; Guijarro, Maria; Ruz, José J.; Cruz, Jesús M.; Montes, Fernando

2009-01-01

This paper describes a novel feature-based stereovision matching process based on a pair of omnidirectional images in forest stands acquired with a stereovision sensor equipped with fish-eye lenses. The stereo analysis problem consists of the following steps: image acquisition, camera modelling, feature extraction, image matching and depth determination. Once the depths of significant points on the trees are obtained, the growing stock volume can be estimated by considering the geometrical camera modelling, which is the final goal. The key steps are feature extraction and image matching. This paper is devoted solely to these two steps. At a first stage a segmentation process extracts the trunks, which are the regions used as features, where each feature is identified through a set of attributes of properties useful for matching. In the second step the features are matched based on the application of the following four well known matching constraints, epipolar, similarity, ordering and uniqueness. The combination of the segmentation and matching processes for this specific kind of sensors make the main contribution of the paper. The method is tested with satisfactory results and compared against the human expert criterion. PMID:22303134

Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences

PubMed Central

Pedraja, Federico; Aguilera, Pedro; Caputi, Angel A.; Budelli, Ruben

2014-01-01

Modeling the electric field and images in electric fish contributes to a better understanding of the pre-receptor conditioning of electric images. Although the boundary element method has been very successful for calculating images and fields, complex electric organ discharges pose a challenge for active electroreception modeling. We have previously developed a direct method for calculating electric images which takes into account the structure and physiology of the electric organ as well as the geometry and resistivity of fish tissues. The present article reports a general application of our simulator for studying electric images in electric fish with heterogeneous, extended electric organs. We studied three species of Gymnotiformes, including both wave-type (Apteronotus albifrons) and pulse-type (Gymnotus obscurus and Gymnotus coropinae) fish, with electric organs of different complexity. The results are compared with the African (Gnathonemus petersii) and American (Gymnotus omarorum) electric fish studied previously. We address the following issues: 1) how to calculate equivalent source distributions based on experimental measurements, 2) how the complexity of the electric organ discharge determines the features of the electric field and 3) how the basal field determines the characteristics of electric images. Our findings allow us to generalize the hypothesis (previously posed for G. omarorum) in which the perioral region and the rest of the body play different sensory roles. While the “electrosensory fovea” appears suitable for exploring objects in detail, the rest of the body is likened to a “peripheral retina” for detecting the presence and movement of surrounding objects. We discuss the commonalities and differences between species. Compared to African species, American electric fish show a weaker field. This feature, derived from the complexity of distributed electric organs, may endow Gymnotiformes with the ability to emit site-specific signals to be detected in the short range by a conspecific and the possibility to evolve predator avoidance strategies. PMID:25010765

Electric imaging through evolution, a modeling study of commonalities and differences.

PubMed

Pedraja, Federico; Aguilera, Pedro; Caputi, Angel A; Budelli, Ruben

2014-07-01

Modeling the electric field and images in electric fish contributes to a better understanding of the pre-receptor conditioning of electric images. Although the boundary element method has been very successful for calculating images and fields, complex electric organ discharges pose a challenge for active electroreception modeling. We have previously developed a direct method for calculating electric images which takes into account the structure and physiology of the electric organ as well as the geometry and resistivity of fish tissues. The present article reports a general application of our simulator for studying electric images in electric fish with heterogeneous, extended electric organs. We studied three species of Gymnotiformes, including both wave-type (Apteronotus albifrons) and pulse-type (Gymnotus obscurus and Gymnotus coropinae) fish, with electric organs of different complexity. The results are compared with the African (Gnathonemus petersii) and American (Gymnotus omarorum) electric fish studied previously. We address the following issues: 1) how to calculate equivalent source distributions based on experimental measurements, 2) how the complexity of the electric organ discharge determines the features of the electric field and 3) how the basal field determines the characteristics of electric images. Our findings allow us to generalize the hypothesis (previously posed for G. omarorum) in which the perioral region and the rest of the body play different sensory roles. While the "electrosensory fovea" appears suitable for exploring objects in detail, the rest of the body is likened to a "peripheral retina" for detecting the presence and movement of surrounding objects. We discuss the commonalities and differences between species. Compared to African species, American electric fish show a weaker field. This feature, derived from the complexity of distributed electric organs, may endow Gymnotiformes with the ability to emit site-specific signals to be detected in the short range by a conspecific and the possibility to evolve predator avoidance strategies.

Quantitative evaluation of macrophage aggregates in brook trout Salvelinus fontinalis and rainbow trout Oncorhynchus mykiss

USGS Publications Warehouse

Schwindt, Adam R.; Truelove, Nathan; Schreck, Carl B.; Fournie, John W.; Landers, Dixon H.; Kent, Michael L.

2006-01-01

Macrophage aggregates (MAs) occur in various organs of fishes, especially the kidney, liver and spleen, and contain melanin, ceroid/lipofuscin and hemosiderin pigments. They have been used as indicators of a number of natural and anthropogenic stressors. Macrophage aggregates occur in salmonids but are poorly organized, irregularly shaped, and are generally smaller than those in derived teleosts. These features complicate quantification, and thus these fishes have seldom been used in studies correlating MAs with environmental stressors. To alleviate these complications, we developed color filtering algorithms for use with the software package ImagePro Plus® (Media Cybernetics) that select and quantify pigmented area (i.e. colors ranging from gold to brown to black) in tissue sections. Image analysis results compared well with subjective scoring when tested on brook trout Salvelinus fontinalis and rainbow trout Oncorhynchus mykiss captured from high-elevation lakes or hatcheries. Macrophage aggregate pigments correlated positively with age and negatively with condition factor. Within individual fish, pigmentation correlated positively among organs, suggesting that the kidney, liver or spleen are suitable indicator organs. In age-matched fishes, MA pigments were not different between hatcheries and lakes in the organs examined. Between lakes, differences in pigments were observed in the kidney and spleen, but were not explained by age, condition factor, sex or maturation state. Our results indicate that quantification of the area occupied by MA pigments is an efficient and accurate means of evaluating MAs in salmonid organs and that organ pigmentation correlates with age and condition factor, as seen in studies with more derived fishes. 

Minerals and aligned collagen fibrils in tilapia fish scales: structural analysis using dark-field and energy-filtered transmission electron microscopy and electron tomography.

PubMed

Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki

2011-10-01

The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.

A retrospective on hydroacoustic assessment of fish passage in Alaskan rivers

NASA Astrophysics Data System (ADS)

Burwen, Debby; Fleischman, Steve; Maxwell, Suzanne; Pfisterer, Carl

2005-04-01

The Alaska Department of Fish and Game (ADFG) has enumerated fish stocks in rivers for over 30 years using a variety of acoustic technologies including single-, dual-, and split-beam sonar. Most recently, ADFG has evaluated a relatively new sonar technology at several sites in Alaska to determine its applicability to counting migrating fish in rivers. The new system, called a Dual frequency IDentification SONar (DIDSON), is a high-definition imaging sonar designed and manufactured by the University of Washington's Applied Physics Lab for military applications such as diver detection and underwater mine identification. Results from experiments conducted in 2002-2004 indicate that DIDSON provides significant improvements in our ability to detect, track, and determine the direction of travel of migrating fish in rivers. One of the most powerful uses of the DIDSON has been to combine its camera-like images of fish swimming behavior with corresponding split-beam data. These linked datasets have allowed us to evaluate the effects of fish orientation and swimming behavior on echo shape parameters that have proven useful in the classification of certain fish species.

Frequency dependence and passive drains in fish-eye lenses

NASA Astrophysics Data System (ADS)

Quevedo-Teruel, O.; Mitchell-Thomas, R. C.; Hao, Y.

2012-11-01

The Maxwell fish eye lens has previously been reported as being capable of the much sought after phenomenon of subwavelength imaging. The inclusion of a drain in this system is considered crucial to the imaging ability, although its role is the topic of much debate. This paper provides a numerical investigation into a practical implementation of a drain in such systems, and analyzes the strong frequency dependence of both the Maxwell fish eye lens and an alternative, the Miñano lens. The imaging capability of these types of lens is questioned, and it is supported by simulations involving various configurations of drain arrays. Finally, a discussion of the near-field and evanescent wave contribution is given.

Fluorescent ligand fishing combination with in-situ imaging and characterizing to screen Hsp 90 inhibitors from Curcuma longa L. based on InP/ZnS quantum dots embedded mesoporous nanoparticles.

PubMed

Hu, Yue; Fu, Anchen; Miao, Zhaoyi; Zhang, Xiaojing; Wang, Tianlin; Kang, An; Shan, Jinjun; Zhu, Dong; Li, Wei

2018-02-01

Although ligand fishing has been shown to be an efficient technique for the identification of bioactive components from complex mixtures such as natural products, it cannot be applied to biomedical image processing. Herein, a specific fluorescent ligand fishing combined with in situ imaging approach is presented for the identification of heat shock protein 90 (Hsp 90) inhibitors from complex matrixes, Curcuma longa L., using N-terminus immobilized Hsp 90α functionalized InP/ZnS quantum dots embedded mesoporous nanoparticles (i.e. Hsp 90α (NT)-FQDNs) as extraction sorbents and fluorescent tracer. The fished ligands were identified by liquid chromatography time-of-flight/mass spectrometry (LC-TOF/MS) and gas chromatography-mass spectrometry (GC-MS). Moreover, in situ imaging by confocal laser scanning microscopy (CLSM) was applied for evaluating the effect of fished-ligands on bioactivity-induced apoptosis morphologically in HeLa cells. MTT assay verified the bioactivity of the ligands and molecular docking results further provided convincing information to verify the feasible binding mode between ligands and protein. Twelve ligands as potential Hsp 90 inhibitors were ultimately fished and identified from Curcuma longa L. crude extracts. The proposed approach based on Hsp 90α functionalized nanocomposites is superior in the combination of highly specific screening efficiency and concurrent visual in situ imaging, which could have great promise for the development of other plant-derived Hsp 90 inhibitors, and providing a rapid and reliable platform for discovering biologically active molecules in natural products. Copyright © 2017 Elsevier B.V. All rights reserved.

Proteomic sensitivity to dietary manipulations in rainbow trout.

PubMed

Martin, S A M; Vilhelmsson, O; Médale, F; Watt, P; Kaushik, S; Houlihan, D F

2003-09-23

Changes in dietary protein sources due to substitution of fish meal by other protein sources can have metabolic consequences in farmed fish. A proteomics approach was used to study the protein profiles of livers of rainbow trout that have been fed two diets containing different proportions of plant ingredients. Both diets control (C) and soy (S) contained fish meal and plant ingredients and synthetic amino acids, but diet S had a greater proportion of soybean meal. A feeding trial was performed for 12 weeks at the end of which, growth and protein metabolism parameters were measured. Protein growth rates were not different in fish fed different diets; however, protein consumption and protein synthesis rates were higher in the fish fed the diet S. Fish fed diet S had lower efficiency of retention of synthesised protein. Ammonia excretion was increased as well as the activities of hepatic glutamate dehydrogenase and aspartate amino transferase (ASAT). No differences were found in free amino acid pools in either liver or muscle between diets. Protein extraction followed by high-resolution two-dimensional electrophoresis, coupled with gel image analysis, allowed identification and expression of hundreds of protein. Individual proteins of interest were then subjected to further analysis leading to protein identification by trypsin digest fingerprinting. During this study, approximately 800 liver proteins were analysed for expression pattern, of which 33 were found to be differentially expressed between diets C and S. Seventeen proteins were positively identified after database searching. Proteins were identified from diverse metabolic pathways, demonstrating the complex nature of gene expression responses to dietary manipulation revealed by proteomic characterisation.

Ocular anatomy of the black pacu (Colossoma macropomum): gross, histologic, and diagnostic imaging.

PubMed

Gustavsen, Kate A; Paul-Murphy, Joanne R; Weber, Ernest Scott; Zwingenberger, Allison L; Dunker, Freeland H; Dubielzig, Richard R; Reilly, Christopher M; Murphy, Christopher J

2018-01-30

To describe the ocular anatomy of the black pacu (Colossoma macropomum), a freshwater teleost fish of the Amazon River basin, including an unusual choroid laden with adipose tissue. Three adult black pacu were anesthetized and examined clinically and with ocular ultrasonography, then euthanized. Three fish were euthanized and their heads imaged immediately postmortem using computed tomography. One fish was euthanized and its exenterated eyes imaged by high-resolution magnetic resonance imaging. The exenterated eyes of all seven fish were fixed in formalin; eyes from three fish were examined grossly and histologically. Additionally, archived histologic sections from two smaller black pacu specimens were examined. Findings were consistent among the ocular imaging modalities used. Intrinsic to the sclera were circumferential ossicles and scleral cartilage. The lens was spherical and protruded through the ovoid pupil with an aphakic space inferiorly when the accommodative mechanism was relaxed under anesthesia. Both a small falciform process and epiretinal vasculature were present in the posterior segment. The retina was cone-rich, and processes of the retinal pigment epithelium enveloped the photoreceptor outer segments. Remarkably, the choroid occupied one-third of the anteroposterior length of the globe; histology confirmed that the bulk of the choroid was composed of adipose tissue. The eye of the pacu overall is typical of teleosts but has the notable and consistent finding of a substantive store of choroidal fat of unknown function. © 2018 American College of Veterinary Ophthalmologists.

A video multitracking system for quantification of individual behavior in a large fish shoal: advantages and limits.

PubMed

Delcourt, Johann; Becco, Christophe; Vandewalle, Nicolas; Poncin, Pascal

2009-02-01

The capability of a new multitracking system to track a large number of unmarked fish (up to 100) is evaluated. This system extrapolates a trajectory from each individual and analyzes recorded sequences that are several minutes long. This system is very efficient in statistical individual tracking, where the individual's identity is important for a short period of time in comparison with the duration of the track. Individual identification is typically greater than 99%. Identification is largely efficient (more than 99%) when the fish images do not cross the image of a neighbor fish. When the images of two fish merge (occlusion), we consider that the spot on the screen has a double identity. Consequently, there are no identification errors during occlusions, even though the measurement of the positions of each individual is imprecise. When the images of these two merged fish separate (separation), individual identification errors are more frequent, but their effect is very low in statistical individual tracking. On the other hand, in complete individual tracking, where individual fish identity is important for the entire trajectory, each identification error invalidates the results. In such cases, the experimenter must observe whether the program assigns the correct identification, and, when an error is made, must edit the results. This work is not too costly in time because it is limited to the separation events, accounting for fewer than 0.1% of individual identifications. Consequently, in both statistical and rigorous individual tracking, this system allows the experimenter to gain time by measuring the individual position automatically. It can also analyze the structural and dynamic properties of an animal group with a very large sample, with precision and sampling that are impossible to obtain with manual measures.

Multispectral Imaging for Determination of Astaxanthin Concentration in Salmonids

PubMed Central

Dissing, Bjørn S.; Nielsen, Michael E.; Ersbøll, Bjarne K.; Frosch, Stina

2011-01-01

Multispectral imaging has been evaluated for characterization of the concentration of a specific cartenoid pigment; astaxanthin. 59 fillets of rainbow trout, Oncorhynchus mykiss, were filleted and imaged using a rapid multispectral imaging device for quantitative analysis. The multispectral imaging device captures reflection properties in 19 distinct wavelength bands, prior to determination of the true concentration of astaxanthin. The samples ranged from 0.20 to 4.34 g per g fish. A PLSR model was calibrated to predict astaxanthin concentration from novel images, and showed good results with a RMSEP of 0.27. For comparison a similar model were built for normal color images, which yielded a RMSEP of 0.45. The acquisition speed of the multispectral imaging system and the accuracy of the PLSR model obtained suggest this method as a promising technique for rapid in-line estimation of astaxanthin concentration in rainbow trout fillets. PMID:21573000

The threshold induction temperature of the 90-kDa heat shock protein is subject to acclimatization in eurythermal goby fishes (genus Gillichthys).

PubMed Central

Dietz, T J; Somero, G N

1992-01-01

Two extremely eurythermal goby fishes, Gillichthys mirabilis and Gillichthys seta, which encounter habitat temperature variations of approximately 30 degrees C, showed seasonal acclimatization of endogenous levels and of onset temperatures for enhanced synthesis of a 90-kDa-class heat shock protein (HSP90). Summer-acclimatized fishes had higher levels of HSP90 in brain tissue than winter-acclimatized specimens, as shown by Western blot analysis. For winter-acclimatized fishes, increased synthesis of HSP90 was observed when the temperature was raised from a control temperature (18 degrees C) to 28 degrees C. For summer-acclimatized fish, no significantly increased synthesis of HSP90 occurred until the experimental temperature was raised to 32 degrees C. These data suggest that the threshold temperature at which enhanced expression of HSP-encoding genes occurs is not hard-wired genetically but may be subject to acclimatization. A causal relationship between seasonal changes in steady-state levels of HSP90 and the threshold temperature for enhanced HSP90 synthesis is discussed in terms of existing models for the regulation of HSP gene expression. Images PMID:1565632

Discrimination between weaned and unweaned Atlantic cod (Gadus morhua) in capture-based aquaculture (CBA) by X-ray imaging and radio-frequency metal detector.

PubMed

Misimi, Ekrem; Martinsen, Svein; Mathiassen, John Reidar; Erikson, Ulf

2014-01-01

The aim of this study was to investigate the feasibility of two detection methods for use in discrimination and sorting of adult Atlantic cod (about 2 kg) in the small scale capture-based aquaculture (CBA). Presently, there is no established method for discrimination of weaned and unweaned cod in CBA. Generally, 60-70% of the wild-caught cod in the CBA are weaned into commercial dry feed. To increase profitability for the fish farmers, unweaned cod must be separated from the stock, meaning the fish must be sorted into two groups - unweaned and weaned from moist feed. The challenges with handling of large numbers of fish in cages, defined the limits of the applied technology. As a result, a working model was established, focusing on implementing different marking materials added to the fish feed, and different technology for detecting the feed presence in the fish gut. X-ray imaging in two modes (planar and dual energy band) and sensitive radio-frequency metal detection were the detection methods that were chosen for the investigations. Both methods were tested in laboratory conditions using dead fish with marked feed inserted into the gut cavity. In particular, the sensitive radio-frequency metal detection method with carbonyl powder showed very promising results in detection of marked feed. Results show also that Dual energy band X-ray imaging may have potential for prediction of fat content in the feed. Based on the investigations it can be concluded that both X-ray imaging and sensitive radio-frequency metal detector technology have the potential for detecting cod having consumed marked feed. These are all technologies that may be adapted to large scale handling of fish from fish cages. Thus, it may be possible to discriminate between unweaned and weaned cod in a large scale grading situation. Based on the results of this study, a suggestion for evaluation of concept for in-situ sorting system is presented.

Potential impacts of the Deepwater Horizon oil spill on large pelagic fishes

NASA Astrophysics Data System (ADS)

Frias-Torres, Sarrah; Bostater, Charles R., Jr.

2011-11-01

Biogeographical analyses provide insights on how the Deepwater Horizon oil spill impacted large pelagic fishes. We georeferenced historical ichthyoplankton surveys and published literature to map the spawning and larval areas of bluefin tuna, swordfish, blue marlin and whale shark sightings in the Gulf of Mexico with daily satellite-derived images detecting surface oil. The oil spill covered critical areas used by large pelagic fishes. Surface oil was detected in 100% of the northernmost whale shark sightings, in 32.8 % of the bluefin tuna spawning area and 38 % of the blue marlin larval area. No surface oil was detected in the swordfish spawning and larval area. Our study likely underestimates the extend of the oil spill due to satellite sensors detecting only the upper euphotic zone and the use of dispersants altering crude oil density, but provides a previously unknown spatio-temporal analysis.

50 CFR 270.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... restaurant trade, but whose primary business function is not the processing or packaging of fish or fish... processing vessels and any person in the business of acquiring (taking title to) fish directly from harvesters. Research means any type of research designed to advance the image, desirability, usage...

50 CFR 270.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... restaurant trade, but whose primary business function is not the processing or packaging of fish or fish... processing vessels and any person in the business of acquiring (taking title to) fish directly from harvesters. Research means any type of research designed to advance the image, desirability, usage...

50 CFR 270.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... restaurant trade, but whose primary business function is not the processing or packaging of fish or fish... processing vessels and any person in the business of acquiring (taking title to) fish directly from harvesters. Research means any type of research designed to advance the image, desirability, usage...

50 CFR 270.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... restaurant trade, but whose primary business function is not the processing or packaging of fish or fish... processing vessels and any person in the business of acquiring (taking title to) fish directly from harvesters. Research means any type of research designed to advance the image, desirability, usage...

50 CFR 270.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... restaurant trade, but whose primary business function is not the processing or packaging of fish or fish... processing vessels and any person in the business of acquiring (taking title to) fish directly from harvesters. Research means any type of research designed to advance the image, desirability, usage...

Predicting Fish Growth Potential and Identifying Water Quality Constraints: A Spatially-Explicit Bioenergetics Approach

NASA Astrophysics Data System (ADS)

Budy, Phaedra; Baker, Matthew; Dahle, Samuel K.

2011-10-01

Anthropogenic impairment of water bodies represents a global environmental concern, yet few attempts have successfully linked fish performance to thermal habitat suitability and fewer have distinguished co-varying water quality constraints. We interfaced fish bioenergetics, field measurements, and Thermal Remote Imaging to generate a spatially-explicit, high-resolution surface of fish growth potential, and next employed a structured hypothesis to detect relationships among measures of fish performance and co-varying water quality constraints. Our thermal surface of fish performance captured the amount and spatial-temporal arrangement of thermally-suitable habitat for three focal species in an extremely heterogeneous reservoir, but interpretation of this pattern was initially confounded by seasonal covariation of water residence time and water quality. Subsequent path analysis revealed that in terms of seasonal patterns in growth potential, catfish and walleye responded to temperature, positively and negatively, respectively; crappie and walleye responded to eutrophy (negatively). At the high eutrophy levels observed in this system, some desired fishes appear to suffer from excessive cultural eutrophication within the context of elevated temperatures whereas others appear to be largely unaffected or even enhanced. Our overall findings do not lead to the conclusion that this system is degraded by pollution; however, they do highlight the need to use a sensitive focal species in the process of determining allowable nutrient loading and as integrators of habitat suitability across multiple spatial and temporal scales. We provide an integrated approach useful for quantifying fish growth potential and identifying water quality constraints on fish performance at spatial scales appropriate for whole-system management.

A high-throughput lab-on-a-chip interface for zebrafish embryo tests in drug discovery and ecotoxicology

NASA Astrophysics Data System (ADS)

Zhu, Feng; Akagi, Jin; Hall, Chris J.; Crosier, Kathryn E.; Crosier, Philip S.; Delaage, Pierre; Wlodkowic, Donald

2013-12-01

Drug discovery screenings performed on zebrafish embryos mirror with a high level of accuracy. The tests usually performed on mammalian animal models, and the fish embryo toxicity assay (FET) is one of the most promising alternative approaches to acute ecotoxicity testing with adult fish. Notwithstanding this, conventional methods utilising 96-well microtiter plates and manual dispensing of fish embryos are very time-consuming. They rely on laborious and iterative manual pipetting that is a main source of analytical errors and low throughput. In this work, we present development of a miniaturised and high-throughput Lab-on-a-Chip (LOC) platform for automation of FET assays. The 3D high-density LOC array was fabricated in poly-methyl methacrylate (PMMA) transparent thermoplastic using infrared laser micromachining while the off-chip interfaces were fabricated using additive manufacturing processes (FDM and SLA). The system's design facilitates rapid loading and immobilization of a large number of embryos in predefined clusters of traps during continuous microperfusion of drugs/toxins. It has been conceptually designed to seamlessly interface with both upright and inverted fluorescent imaging systems and also to directly interface with conventional microtiter plate readers that accept 96-well plates. We also present proof-of-concept interfacing with a high-speed imaging cytometer Plate RUNNER HD® capable of multispectral image acquisition with resolution of up to 8192 x 8192 pixels and depth of field of about 40 μm. Furthermore, we developed a miniaturized and self-contained analytical device interfaced with a miniaturized USB microscope. This system modification is capable of performing rapid imaging of multiple embryos at a low resolution for drug toxicity analysis.

Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).

PubMed

Salimi, Nima; Loh, Kar Hoe; Kaur Dhillon, Sarinder; Chong, Ving Ching

2016-01-01

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

Single-cell in vivo imaging of adult neural stem cells in the zebrafish telencephalon.

PubMed

Barbosa, Joana S; Di Giaimo, Rossella; Götz, Magdalena; Ninkovic, Jovica

2016-08-01

Adult neural stem cells (aNSCs) in zebrafish produce mature neurons throughout their entire life span in both the intact and regenerating brain. An understanding of the behavior of aNSCs in their intact niche and during regeneration in vivo should facilitate the identification of the molecular mechanisms controlling regeneration-specific cellular events. A greater understanding of the process in regeneration-competent species may enable regeneration to be achieved in regeneration-incompetent species, including humans. Here we describe a protocol for labeling and repetitive imaging of aNSCs in vivo. We label single aNSCs, allowing nonambiguous re-identification of single cells in repetitive imaging sessions using electroporation of a red-reporter plasmid in Tg(gfap:GFP)mi2001 transgenic fish expressing GFP in aNSCs. We image using two-photon microscopy through the thinned skull of anesthetized and immobilized fish. Our protocol allows imaging every 2 d for a period of up to 1 month. This methodology allowed the visualization of aNSC behavior in vivo in their natural niche, in contrast to previously available technologies, which rely on the imaging of either dissociated cells or tissue slices. We used this protocol to follow the mode of aNSC division, fate changes and cell death in both the intact and injured zebrafish telencephalon. This experimental setup can be widely used, with minimal prior experience, to assess key factors for processes that modulate aNSC behavior. A typical experiment with data analysis takes up to 1.5 months.

Extraction of high value added gelatin biopolymer from black tilapia (Oreochromis mossambicus) head bones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sockalingam, K., E-mail: gd130106@siswa.uthm.edu.my; Abdullah, H. Z., E-mail: hasan@uthm.edu.my

Black tilapia (Oreochromis mossambicus) fish head bones were evaluated for its possibilities in extracting gelatin. Head bones were subjected to pre-treatment with 3% of hydrochloric acid (HCl) for demineralization before undergoes thermal extraction process. The raw head bones were characterized via Scanning Electron Microscopy (SEM) in order to investigate the external and internal surface morphology. SEM images also reveal the presence of collagen fiber with 1 µm diameter in the head bone. The black tilapia fish head bones yields 5.75 % of gelatin in wet weight basis, indicating the possibility of this fish species as sources of gelatin. Further characterizations weremore » done on both raw head bones and extracted gelatin through Fourier Transform Infrared Spectroscopy (FTIR) and proximate analysis. The head bones gelatin shows high protein (10.55%) and ash (3.11 %) content with low moisture. This further proves the effectiveness of demineralization and extraction method used. The black tilapia fish head bones are found to be a prospective source of gelatin with good chemical and functional properties.« less

Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as.

PubMed

Kocks, Christine; Boltengagen, Anastasiya; Piwecka, Monika; Rybak-Wolf, Agnieszka; Rajewsky, Nikolaus

2018-01-01

Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.

Remote Sensing of Marine Life and Submerged Target Motions with Ocean Waveguide Acoustics

NASA Astrophysics Data System (ADS)

Gong, Zheng

Many species of fish that inhabit the continental shelf waters can cause significant acoustic scattering at low- to mid-frequencies due to the large impedance contrast between their air-filled swimbladders and the surrounding water. In this thesis, we investigate the acoustic resonance scattering response from distributed fish groups both experimentally and theoretically including the effects of multiple scattering, attenuation, and dispersion in a random range-dependent ocean waveguide using an instantaneous wide-area imaging system. In navy sonar operations, the biological organisms can cause high false alarm rates or missed target detections since the biological scattering can be confused with or camouflage the returns from other discrete and distributed objects, such as underwater vehicles and geologic features. From an ecological perspective, the ability to instantaneously survey fish populations distributed over wide areas is important for fisheries management. The low-frequency target strength of shoaling Atlantic herring ( Clupea harengus) in the Gulf of Maine during their Autumn 2006 spawning season is estimated from experimental data acquired simultaneously at multiple frequencies in the 300 to 1200 Hz range using (1) a low-frequency ocean acoustic waveguide remote sensing (OAWRS) system, (2) areal population density calibration with several conventional fish finding sonar (CFFS) systems, and (3) low-frequency transmission loss measurements. The OAWRS system's instantaneous imaging diameter of 100 km and regular updating enabled unaliased monitoring of fish populations over ecosystem scales including shoals of Atlantic herring containing as many as 200 million individuals, as estimated based on single scattering assumption and confirmed by concurrent trawl and CFFS sampling. The mean scattering cross-section of an individual shoaling herring is found to consistently exhibit a strong, roughly 20 dB/octave roll-off with decreasing frequency over all days of the roughly 2-week experiment, consistent with the steep roll-offs expected for sub-resonance scattering from fish with air-filled swimbladders. A numerical Monte-Carlo model is developed to determine the statistical moments of the broadband matched filtered scattered returns from fish groups spanning over multiple range and cross-range resolution cells of a waveguide remote sensing system. It uses the parabolic equation to simulate acoustic field propagation in a random range-dependent ocean waveguide. The effects of (1) multiple scattering, (2) attenuation due to scattering, and (3) fish group 3D spatial configuration on fish population density imaging are examined. The model is applied to investigate (a) population density imaging of shoaling Atlantic herring during the 2006 Gulf of Maine Experiment (GOME06) and (b) examine the wide-area imaging of sparse aggregation of ground fish species, such as Atlantic Cod, in Ipswich Bay continental shelf environment using the waveguide remote sensing system. Incoherent intensities are shown to dominate the total scattered returns from distributed fish groups making single scattering assumption valid for inferring fish areal population densities from their matched filtered scattered intensities. Multiple scattering, attenuation, fish group 3D spatial configuration, and coherent effects, such as resonance shift, sub- and super-local-maxima are found to be negligible at the imaging frequencies employed and for the herring densities observed. Similar results are obtained for the sparsely aggregated cod, but coherent effects such as the double-peak in school resonance can be prominent at much lower fish densities. Attenuation due to scattering can be significant when the fish flesh viscosity is high, especially true for cod. We also investigate approaches for instantaneous long-range passive source localization and tracking with a towed horizontal line-array in a random range-dependent ocean waveguide using passive waveguide acoustics. This is very important for many sonar applications, such as localizing and tracking underwater vehicles and vocalizing marine mammal populations. Instantaneous passive source localization applying the (1) synthetic aperture tracking, (2) array invariant, (3) bearings-only target motion analysis in modified polar coordinates via the extended Kalman filter, and (4) bearings-migration minimum mean-square error methods using measurements made on a single towed horizontal receiver array in a random range-dependent ocean waveguide are examined. These methods are employed to localize and track a vertical source array deployed in the far-field of a towed horizontal receiver array during the Gulf of Maine 2006 Experiment. The source transmitted intermittent broadband pulses in the 300--1200 Hz frequency range. All four methods are found to be comparable with average errors of between 9% to 13% in estimating the mean source positions in a wide variety of source-receiver geometries and range separations up to 20 km. In the case of a relatively stationary source, the synthetic aperture tracking outperformed the other three methods by a factor of two with only 4% error. For a moving source, the Kalman filter method yielded the best performance with 8% error. The array invariant was the best approach for localizing sources within the endfire beam of the receiver array with less than 10% error.

Computed tomographic and cross-sectional anatomy of the normal pacu (Colossoma macroponum).

PubMed

Carr, Alaina; Weber, E P Scott; Murphy, Chris J; Zwingenberger, Alison

2014-03-01

The purpose of this study was to compare and define the normal cross-sectional gross and computed tomographic (CT) anatomy for a species of boney fish to better gain insight into the use of advanced diagnostic imaging for future clinical cases. The pacu (Colossoma macropomum) was used because of its widespread presence in the aquarium trade, its relatively large body size, and its importance in the research and aquaculture settings. Transverse 0.6-mm CT images of three cadaver fish were obtained and compared to corresponding frozen cross sections of the fish. Relevant anatomic structures were identified and labeled at each level; the Hounsfield unit density of major organs was established. The images presented good anatomic detail and provide a reference for future research and clinical investigation.

Reliability of fish size estimates obtained from multibeam imaging sonar

USGS Publications Warehouse

Hightower, Joseph E.; Magowan, Kevin J.; Brown, Lori M.; Fox, Dewayne A.

2013-01-01

Multibeam imaging sonars have considerable potential for use in fisheries surveys because the video-like images are easy to interpret, and they contain information about fish size, shape, and swimming behavior, as well as characteristics of occupied habitats. We examined images obtained using a dual-frequency identification sonar (DIDSON) multibeam sonar for Atlantic sturgeon Acipenser oxyrinchus oxyrinchus, striped bass Morone saxatilis, white perch M. americana, and channel catfish Ictalurus punctatus of known size (20–141 cm) to determine the reliability of length estimates. For ranges up to 11 m, percent measurement error (sonar estimate – total length)/total length × 100 varied by species but was not related to the fish's range or aspect angle (orientation relative to the sonar beam). Least-square mean percent error was significantly different from 0.0 for Atlantic sturgeon (x̄  =  −8.34, SE  =  2.39) and white perch (x̄  = 14.48, SE  =  3.99) but not striped bass (x̄  =  3.71, SE  =  2.58) or channel catfish (x̄  = 3.97, SE  =  5.16). Underestimating lengths of Atlantic sturgeon may be due to difficulty in detecting the snout or the longer dorsal lobe of the heterocercal tail. White perch was the smallest species tested, and it had the largest percent measurement errors (both positive and negative) and the lowest percentage of images classified as good or acceptable. Automated length estimates for the four species using Echoview software varied with position in the view-field. Estimates tended to be low at more extreme azimuthal angles (fish's angle off-axis within the view-field), but mean and maximum estimates were highly correlated with total length. Software estimates also were biased by fish images partially outside the view-field and when acoustic crosstalk occurred (when a fish perpendicular to the sonar and at relatively close range is detected in the side lobes of adjacent beams). These sources of bias are apparent when files are processed manually and can be filtered out when producing automated software estimates. Multibeam sonar estimates of fish size should be useful for research and management if these potential sources of bias and imprecision are addressed.

Fisheries imaging radar surveillance test /FIRST/ - Bering Sea test

NASA Technical Reports Server (NTRS)

Woods, E. G.; Ivey, J. H.

1977-01-01

A joint NOAA, U.S. Coast Guard and NASA program is being conducted to determine if a synthetic aperture radar (SAR) system, such as planned for NASA's SEASAT, can be useful in monitoring fishing vessels within the newly established 200-mile fishing limit. As part of this program, data gathering field operations were conducted over concentrations of foreign fishing vessels in the Bering Sea off Alaska in April 1976. The Jet Propulsion Laboratory developed synthetic aperture L-band radar which was flown aboard the NASA Convair 990 aircraft, with a Coast Guard cutter and C-130 aircraft simultaneously gathering data to provide both radar imagery and sea truth information on the vessels being imaged. Results indicate that synthetic aperture radar systems have potential for all weather detection, enumeration and classification of fishing vessels.

Soundscapes and the sense of hearing of fishes.

PubMed

Fay, Richard

2009-03-01

Underwater soundscapes have probably played an important role in the adaptation of ears and auditory systems of fishes throughout evolutionary time, and for all species. These sounds probably contain important information about the environment and about most objects and events that confront the receiving fish so that appropriate behavior is possible. For example, the sounds from reefs appear to be used by at least some fishes for their orientation and migration. These sorts of environmental sounds should be considered much like "acoustic daylight," that continuously bathes all environments and contain information that all organisms can potentially use to form a sort of image of the environment. At present, however, we are generally ignorant of the nature of ambient sound fields impinging on fishes, and the adaptive value of processing these fields to resolve the multiple sources of sound. Our field has focused almost exclusively on the adaptive value of processing species-specific communication sounds, and has not considered the informational value of ambient "noise." Since all fishes can detect and process acoustic particle motion, including the directional characteristics of this motion, underwater sound fields are potentially more complex and information-rich than terrestrial acoustic environments. The capacities of one fish species (goldfish) to receive and make use of such sound source information have been demonstrated (sound source segregation and auditory scene analysis), and it is suggested that all vertebrate species have this capacity. A call is made to better understand underwater soundscapes, and the associated behaviors they determine in fishes. © 2009 ISZS, Blackwell Publishing and IOZ/CAS.

A Unified Approach to Passive and Active Ocean Acoustic Waveguide Remote Sensing

DTIC Science & Technology

2012-09-30

acoustic sensing reveals humpback whale behavior synchronous with herring spawning processes and sonar had no effect on humpback song ,” submitted to...source and receiver arrays to enable instantaneous continental-shelf scale imaging and continuous monitoring of fish and whale populations. Acoustic...Preliminary analysis shows that humpback whale behavior is synchronous with peak annual Atlantic herring spawning processes in the Gulf of

Microscopy and Image Analysis.

PubMed

McNamara, George; Difilippantonio, Michael; Ried, Thomas; Bieber, Frederick R

2017-07-11

This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy-we briefly point to these new opportunities. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

SEM/EDS and optical microscopy analyses of microplastics in ocean trawl and fish guts.

PubMed

Wang, Zhong-Min; Wagner, Jeff; Ghosal, Sutapa; Bedi, Gagandeep; Wall, Stephen

2017-12-15

Microplastic particles from Atlantic and Pacific Ocean trawls, lab-fed fish guts and ocean fish guts have been characterized using optical microscopy and SEM/EDS in terms of size, morphology, and chemistry. We assessed whether these measurements could serve as a rapid screening process for subsequent identification of the likely microplastic candidates by micro-spectroscopy. Optical microscopy enabled morphological classification of the types of particles or fibers present in the sample, as well as the quantification of particle size ranges and fiber lengths. SEM/EDS analysis was used to rule out non-plastic particles and screen the prepared samples for potential microplastic, based on their element signatures and surface characteristics. Chlorinated plastics such as polyvinyl chloride (PVC) could be easily identified with SEM/EDS due to their unique elemental signatures including chlorine, as could mineral species that are falsely identified as plastics by optical microscopy. Particle morphology determined by optical microscopy and SEM suggests the fish ingested particles contained both degradation fragments from larger plastic pieces and also manufactured microplastics. SEM images of microplastic particle surfaces revealed characteristic cracks consistent with environmental exposure, as well as pigment particles consistent with manufactured materials. Most of the microplastic surfaces in the fish guts and ocean trawls were covered with biofilms, radiolarians, and crustaceans. Many of the fish stomachs contained micro-shell pieces which visually resembled microplastics. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantifying Acoustic Uncertainty due to Marine Mammals and Fish Near the Shelfbreak Front off Cape Hatteras

DTIC Science & Technology

2016-10-19

SUPPLEMENTARY NOTES NA 14. ABSTRACT See attached. 15. SUBJECTTERMS Ocean Acoustics, Fish Scatter, Acoustic Propagation, Oceanography 16...imaging fish schools and tracking vocalizing marine mam mals, and 3) understand the correlation between the detailed physica l oceanography and the...Cape Hatteras, N.C. to measure the acoustics, biology, and physica l oceanography of fish schools) and 2) finish publishing our results. APPROACH

Validation of potential fishing zone forecast using experimental fishing method in Tolo Bay, Central Sulawesi Province

NASA Astrophysics Data System (ADS)

Rintaka, W. E.; Susilo, E.

2018-04-01

The national scale of Indonesian Potential Fishing Zone (PFZ) forecast system has been established since 2000. Recent times this system use Single Image Edge Detection algorithm to automatically identify thermal front from remote sensing images. Its generate two fishing ground/FG criteria: FG (high probability) and potential fishing ground/PFG (medium/low probability). To quantify the accuracy of this algorithm, an experimental fishing/EF was carried out in Tolo Bay, Central Sulawesi Province at September 2016 the late southeast monsoon period by using a pole and line fishing vessel. Four fishing activities (P1, P2, P3, and P4) were conducted during this study at a different location nearby the PFZ forecast position, two of them had good results. Based on distance measurement, these locations P1 and P4 were associated with PFZ forecast position. They were associated with PFG and FG criteria. The distance between EF to P1 and P4 were 9.7 and 6.69 nautical miles. The amount of catch for each location was 850 and 900 kg, respectively. The other locations P2 and P3 were also associated with PFG criteria, but there was no catch. We conclude that the number of the catch is influenced by the distance from PFZ forecast position and criteria.

Multi-camera volumetric PIV for the study of jumping fish

NASA Astrophysics Data System (ADS)

Mendelson, Leah; Techet, Alexandra H.

2018-01-01

Archer fish accurately jump multiple body lengths for aerial prey from directly below the free surface. Multiple fins provide combinations of propulsion and stabilization, enabling prey capture success. Volumetric flow field measurements are crucial to characterizing multi-propulsor interactions during this highly three-dimensional maneuver; however, the fish's behavior also drives unique experimental constraints. Measurements must be obtained in close proximity to the water's surface and in regions of the flow field which are partially-occluded by the fish body. Aerial jump trajectories must also be known to assess performance. This article describes experiment setup and processing modifications to the three-dimensional synthetic aperture particle image velocimetry (SAPIV) technique to address these challenges and facilitate experimental measurements on live jumping fish. The performance of traditional SAPIV algorithms in partially-occluded regions is characterized, and an improved non-iterative reconstruction routine for SAPIV around bodies is introduced. This reconstruction procedure is combined with three-dimensional imaging on both sides of the free surface to reveal the fish's three-dimensional wake, including a series of propulsive vortex rings generated by the tail. In addition, wake measurements from the anal and dorsal fins indicate their stabilizing and thrust-producing contributions as the archer fish jumps.

Determining Suction Feeding Efficiency in the Bowfin fish (Amia) using Particle Image Velocimery and Computaional Fluid Dynamics

NASA Astrophysics Data System (ADS)

Rua, Yenny; Kharbouch, Karim; Sanford, Christopher; Reckinger, Shanon

2014-11-01

Suction feeding is the most common form of prey capture in aquatic vertebrates. During the early evolution of fishes there was a major change in shape of the mouth, from a wedge shaped mouth opening in more primitive fishes to a more circular and planar mouth. This change in shape resulted from increased mobility of a key upper jaw bone, the maxilla. It has been suggested that this change in shape dramatically increased suction feeding efficiency. This study examines the hydrodynamic effects of these two mouth shapes in the same animal, the bowfin fish (Amia calva). 2D Particle Image Velocimetry (PIV) is used to analyze suction feeding events. Post-processing algorithms have been developed to determine the flow rate of water into the mouth of the fish; the area of fluid, the velocity of fluid and the volume of fluid affected by the fish; the velocity of the fluid at the mouth, as well as the velocity of the fluid as a function of the distance from the mouth, finally the force exerted on the fluid by the fish is also determined. Lastly, a numerical model has been developed for comparison using a non-uniform mesh, which adapts dynamically in space and time to the fish feeding event. The realistic geometry of the fish's head is modeled in CAD.

Fluorescence imaging of chromosomal DNA using click chemistry

NASA Astrophysics Data System (ADS)

Ishizuka, Takumi; Liu, Hong Shan; Ito, Kenichiro; Xu, Yan

2016-09-01

Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.

Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF).

PubMed

Honeker, Linnea K; Root, Robert A; Chorover, Jon; Maier, Raina M

2016-12-01

Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME μXRF. The FISH and ME μXRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49±0.19) than to bacteria (0.072±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate. Copyright © 2016 Elsevier B.V. All rights reserved.

Biting cleaner fish use altruism to deceive image-scoring client reef fish.

PubMed Central

Bshary, Redouan

2002-01-01

Humans are more likely to help those who they have observed helping others previously. Individuals may thus benefit from being altruistic without direct reciprocity of recipients but due to gains in 'image' and associated indirect reciprocity. I suggest, however, that image-scoring individuals may be exploitable by cheaters if pay-offs vary between interactions. I illustrate this point with data on cleaner-client reef fish interactions. I show the following: (i) there is strong variation between cleaners with respect to cheating of clients (i.e. feeding on client tissue instead of parasites); (ii) clients approach cleaners, that they observe cooperating with their current client and avoid cleaners that they observe cheating; (iii) cleaners that cheat frequently are avoided more frequently than more cooperative cleaners (iv) cleaners that cheat frequently behave altruistically towards their smallest client species; (v) altruistic acts are followed by exploitative interactions. Thus, it appears that cleaners indeed have an image score, which selects for cooperative cleaners. However, cheating cleaners use altruism in potentially low-pay-off interactions to deceive and attract image-scoring clients that will be exploited. PMID:12396482

Electric organ discharges and electric images during electrolocation

NASA Technical Reports Server (NTRS)

Assad, C.; Rasnow, B.; Stoddard, P. K.

1999-01-01

Weakly electric fish use active electrolocation - the generation and detection of electric currents - to explore their surroundings. Although electrosensory systems include some of the most extensively understood circuits in the vertebrate central nervous system, relatively little is known quantitatively about how fish electrolocate objects. We believe a prerequisite to understanding electrolocation and its underlying neural substrates is to quantify and visualize the peripheral electrosensory information measured by the electroreceptors. We have therefore focused on reconstructing both the electric organ discharges (EODs) and the electric images resulting from nearby objects and the fish's exploratory behaviors. Here, we review results from a combination of techniques, including field measurements, numerical and semi-analytical simulations, and video imaging of behaviors. EOD maps are presented and interpreted for six gymnotiform species. They reveal diverse electric field patterns that have significant implications for both the electrosensory and electromotor systems. Our simulations generated predictions of the electric images from nearby objects as well as sequences of electric images during exploratory behaviors. These methods are leading to the identification of image features and computational algorithms that could reliably encode electrosensory information and may help guide electrophysiological experiments exploring the neural basis of electrolocation.

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications.

PubMed

Cui, Chenghua; Shu, Wei; Li, Peining

2016-01-01

Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.

High-resolution corneal topography and tomography of fish eye using wide-field white light interference microscopy

NASA Astrophysics Data System (ADS)

Srivastava, Vishal; Nandy, Sreyankar; Singh Mehta, Dalip

2013-04-01

Topography and tomography of fish cornea is reconstructed using high resolution white light interference microscopy. White light interferograms at different depths were recorded by moving the object axially. For each depth position, five phase shifted interferograms were recorded and analyzed. From the reconstructed phase maps, the corneal topography and hence the refractive index was determined and from amplitude images the cross-sectional image of fish cornea was reconstructed. In the present method, we utilize a nearly common-path interference microscope and wide field illumination and hence do not require any mechanical B-scan. Therefore, the phase stability of the recorded data is improved.

Navigation Effects on Asian Carp Movement Past Electric Barrier, Chicago Sanitary and Ship Canal

DTIC Science & Technology

2016-02-01

model was necessary to better address the potential mechanisms for transport of Asian carp. In addition to primarily modeling stunned fish , this...model fish positions that varied within the water column to include bottom, near-surface, and mid-depth placement. As additional information was...in the image represents an identified model fish . In addition , fish could be tracked from one frame to the next frame to calculate their velocity

[Non-destructive detection research for hollow heart of potato based on semi-transmission hyperspectral imaging and SVM].

PubMed

Huang, Tao; Li, Xiao-yu; Xu, Meng-ling; Jin, Rui; Ku, Jing; Xu, Sen-miao; Wu, Zhen-zhong

2015-01-01

The quality of potato is directly related to their edible value and industrial value. Hollow heart of potato, as a physiological disease occurred inside the tuber, is difficult to be detected. This paper put forward a non-destructive detection method by using semi-transmission hyperspectral imaging with support vector machine (SVM) to detect hollow heart of potato. Compared to reflection and transmission hyperspectral image, semi-transmission hyperspectral image can get clearer image which contains the internal quality information of agricultural products. In this study, 224 potato samples (149 normal samples and 75 hollow samples) were selected as the research object, and semi-transmission hyperspectral image acquisition system was constructed to acquire the hyperspectral images (390-1 040 nn) of the potato samples, and then the average spectrum of region of interest were extracted for spectral characteristics analysis. Normalize was used to preprocess the original spectrum, and prediction model were developed based on SVM using all wave bands, the accurate recognition rate of test set is only 87. 5%. In order to simplify the model competitive.adaptive reweighed sampling algorithm (CARS) and successive projection algorithm (SPA) were utilized to select important variables from the all 520 spectral variables and 8 variables were selected (454, 601, 639, 664, 748, 827, 874 and 936 nm). 94. 64% of the accurate recognition rate of test set was obtained by using the 8 variables to develop SVM model. Parameter optimization algorithms, including artificial fish swarm algorithm (AFSA), genetic algorithm (GA) and grid search algorithm, were used to optimize the SVM model parameters: penalty parameter c and kernel parameter g. After comparative analysis, AFSA, a new bionic optimization algorithm based on the foraging behavior of fish swarm, was proved to get the optimal model parameter (c=10. 659 1, g=0. 349 7), and the recognition accuracy of 10% were obtained for the AFSA-SVM model. The results indicate that combining the semi-transmission hyperspectral imaging technology with CARS-SPA and AFSA-SVM can accurately detect hollow heart of potato, and also provide technical support for rapid non-destructive detecting of hollow heart of potato.

C-IMAGE Teachers at Sea Maiden Voyages: Promoting Authentic Scientific Research in the Classroom

NASA Astrophysics Data System (ADS)

Hine, A. C.; Greely, T.; Lodge, A.

2012-12-01

The Center for Integrated Modeling & Analysis of Gulf Ecosystems (C-IMAGE) is one of eight consortia participating in the BP/Gulf of Mexico Research Initiative. C-IMAGE is a comprehensive research consortium of 13 national and international universities tasked with evaluating the environmental impacts of the 2010 Deepwater Horizon Oil Spill (DWH) on coastal ecosystems, the water column and the sea floor. The associated C-IMAGE research cruises provide a unique opportunity for Florida's K12 science educators to participate in the data collection and collaboration process alongside marine scientists as a member of the scientific crew. The mission of the C-IMAGE cruises is to help to answer several fundamental questions about the DWH event and subsequent impacts on the plankton population, reef and fish communities and the microbial communities. Deep sea sediment samples, plankton and fishes collected during these expeditions are the data sources. Sampling activities include the use of the SIPPER plankton sampler, multi-core sediment system and long line surveys to assess fish health. While at sea teachers participate in the at sea research and serve as the ship to shore communicator via social media (FB, Twitter, daily blogs) and LIVE video conferencing with formal and informal classrooms. Marine scientists, post-docs and graduate students participating in the C-IMAGE cruises collaborate with the teacher on board to communicate the science, technology and life at sea experiences to educational and general audiences. Upon return to shore, teachers will translate their At Sea learning experience to understandable inquiry-based lessons about the science and technology encompassing the northern Gulf of Mexico ecology, the DWH event and subsequent impacts. Lessons developed from the cruises will inform a future series of C-IMAGE Teacher Professional Developments during Phase 2 of Outreach activities. The results from three Gulf of Mexico expeditions (Aug-Nov) will be presented: related to teachers' working knowledge of research and sampling procedures as well as metrics for the potential value-added of social media as a mechanism for communicating research with formal and informal audiences. C-IMAGE teachers will engage in research with experts in biological and chemical modeling, marine resource assessment, sedimentary geochemistry and toxicology. This research is made possible by a grant from BP/The Gulf of Mexico Research Initiative. Contract #SA 12-10/GoMRI-007;

Fish measurement using Android smart phone: the example of swamp eel

NASA Astrophysics Data System (ADS)

Chen, Baisong; Fu, Zhuo; Ouyang, Haiying; Sun, Yingze; Ge, Changshui; Hu, Jing

The body length and weight are critical physiological parameters for fishes, especially eel-like fishes like swamp eel(Monopterusalbus).Fast and accurate measuring of body length is significant for swamp eel culturing as well as its resource investigation and protection. This paper presents an Android smart phone-based photogrammetry technology for measuring and estimating the length and weight of swamp eel. This method utilizes the feature that the ratio of lengths of two objects within an image is equal to that of in reality to measure the length of swamp eels. And then, it estimates the weight via a pre-built length-weight regression model. Analysis and experimental results have indicated that this method is a fast and accurate method for length and weight measurements of swamp eel. The cross-validation results shows that the RMSE (root-mean-square error) of total length measurement of swamp eel is0.4 cm, and the RMSE of weight estimation is 11 grams.

miRNA detection at single-cell resolution using microfluidic LNA flow-FISH

DOE PAGES

Wu, Meiye; Piccini, Matthew Ernest; Koh, Chung -Yan; ...

2014-08-20

Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155more » and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. Here, we also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.« less

Fish in the matrix: motor learning in a virtual world.

PubMed

Engert, Florian

2012-01-01

One of the large remaining challenges in the field of zebrafish neuroscience is the establishment of techniques and preparations that permit the recording and perturbation of neural activity in animals that can interact meaningfully with the environment. Since it is very difficult to do this in freely behaving zebrafish, I describe here two alternative approaches that meet this goal via tethered preparations. The first uses head-fixation in agarose in combination with online imaging and analysis of tail motion. In the second method, paralyzed fish are suspended with suction pipettes in mid-water and nerve root recordings serve as indicators for intended locomotion. In both cases, fish can be immersed into a virtual environment and allowed to interact with this virtual world via real or fictive tail motions. The specific examples given in this review focus primarily on the role of visual feedback~- but the general principles certainly extend to other modalities, including proprioception, hearing, balance, and somatosensation.

Fish in the matrix: motor learning in a virtual world

PubMed Central

Engert, Florian

2013-01-01

One of the large remaining challenges in the field of zebrafish neuroscience is the establishment of techniques and preparations that permit the recording and perturbation of neural activity in animals that can interact meaningfully with the environment. Since it is very difficult to do this in freely behaving zebrafish, I describe here two alternative approaches that meet this goal via tethered preparations. The first uses head-fixation in agarose in combination with online imaging and analysis of tail motion. In the second method, paralyzed fish are suspended with suction pipettes in mid-water and nerve root recordings serve as indicators for intended locomotion. In both cases, fish can be immersed into a virtual environment and allowed to interact with this virtual world via real or fictive tail motions. The specific examples given in this review focus primarily on the role of visual feedback~– but the general principles certainly extend to other modalities, including proprioception, hearing, balance, and somatosensation. PMID:23355810

Spines of the porcupine fish: Structure, composition, and mechanical properties.

PubMed

Su, Frances Y; Bushong, Eric A; Deerinck, Thomas J; Seo, Kyungah; Herrera, Steven; Graeve, Olivia A; Kisailus, David; Lubarda, Vlado A; McKittrick, Joanna

2017-09-01

This paper explores the structure, composition, and mechanical properties of porcupine fish spines for the first time. The spine was found to be composed of nanocrystalline hydroxyapatite, protein (collagen), and water using X-ray diffraction, energy-dispersive X-ray spectroscopy, and thermogravimetric analysis. Microstructures have mineralized fibrillar sheets in the longitudinal direction and in a radial orientation in the transverse direction that were observed using light and electron microscopy. Based on the images, the hierarchical structure of the spine shows both concentric and radial reinforcement. Mechanical properties were obtained using cantilever beam and nanoindentation tests. A tapered cantilever beam model was developed and compared to that of a uniform cantilever beam. The tapered beam model showed that while the stresses experienced were similar to those of the uniform beam, the location of the maximum stress was near the distal region of the beam rather than at the base, which allows the porcupine fish to conserve energy and resources if the spine is fractured. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electric fish as natural models for technical sensor systems

NASA Astrophysics Data System (ADS)

von der Emde, Gerhard; Bousack, Herbert; Huck, Christina; Mayekar, Kavita; Pabst, Michael; Zhang, Yi

2009-05-01

Instead of vision, many animals use alternative senses for object detection. Weakly electric fish employ "active electrolocation", during which they discharge an electric organ emitting electrical current pulses (electric organ discharges, EOD). Local EODs are sensed by electroreceptors in the fish's skin, which respond to changes of the signal caused by nearby objects. Fish can gain information about attributes of an object, such as size, shape, distance, and complex impedance. When close to the fish, each object projects an 'electric image' onto the fish's skin. In order to get information about an object, the fish has to analyze the object's electric image by sampling its voltage distribution with the electroreceptors. We now know a great deal about the mechanisms the fish use to gain information about objects in their environment. Inspired by the remarkable capabilities of weakly electric fish in detecting and recognizing objects with their electric sense, we are designing technical sensor systems that can solve similar sensing problems. We applied the principles of active electrolocation to devices that produce electrical current pulses in water and simultaneously sense local current densities. Depending on the specific task, sensors can be designed which detect an object, localize it in space, determine its distance, and measure certain object properties such as material properties, thickness, or material faults. We present first experiments and FEM simulations on the optimal sensor arrangement regarding the sensor requirements e. g. localization of objects or distance measurements. Different methods of the sensor read-out and signal processing are compared.

New MYC IHC Classifier Integrating Quantitative Architecture Parameters to Predict MYC Gene Translocation in Diffuse Large B-Cell Lymphoma

PubMed Central

Dong, Wei-Feng; Canil, Sarah; Lai, Raymond; Morel, Didier; Swanson, Paul E.; Izevbaye, Iyare

2018-01-01

A new automated MYC IHC classifier based on bivariate logistic regression is presented. The predictor relies on image analysis developed with the open-source ImageJ platform. From a histologic section immunostained for MYC protein, 2 dimensionless quantitative variables are extracted: (a) relative distance between nuclei positive for MYC IHC based on euclidean minimum spanning tree graph and (b) coefficient of variation of the MYC IHC stain intensity among MYC IHC-positive nuclei. Distance between positive nuclei is suggested to inversely correlate MYC gene rearrangement status, whereas coefficient of variation is suggested to inversely correlate physiological regulation of MYC protein expression. The bivariate classifier was compared with 2 other MYC IHC classifiers (based on percentage of MYC IHC positive nuclei), all tested on 113 lymphomas including mostly diffuse large B-cell lymphomas with known MYC fluorescent in situ hybridization (FISH) status. The bivariate classifier strongly outperformed the “percentage of MYC IHC-positive nuclei” methods to predict MYC+ FISH status with 100% sensitivity (95% confidence interval, 94-100) associated with 80% specificity. The test is rapidly performed and might at a minimum provide primary IHC screening for MYC gene rearrangement status in diffuse large B-cell lymphomas. Furthermore, as this bivariate classifier actually predicts “permanent overexpressed MYC protein status,” it might identify nontranslocation-related chromosomal anomalies missed by FISH. PMID:27093450

Phase shifting white light interferometry using colour CCD for optical metrology and bio-imaging applications

NASA Astrophysics Data System (ADS)

Upputuri, Paul Kumar; Pramanik, Manojit

2018-02-01

Phase shifting white light interferometry (PSWLI) has been widely used for optical metrology applications because of their precision, reliability, and versatility. White light interferometry using monochrome CCD makes the measurement process slow for metrology applications. WLI integrated with Red-Green-Blue (RGB) CCD camera is finding imaging applications in the fields optical metrology and bio-imaging. Wavelength dependent refractive index profiles of biological samples were computed from colour white light interferograms. In recent years, whole-filed refractive index profiles of red blood cells (RBCs), onion skin, fish cornea, etc. were measured from RGB interferograms. In this paper, we discuss the bio-imaging applications of colour CCD based white light interferometry. The approach makes the measurement faster, easier, cost-effective, and even dynamic by using single fringe analysis methods, for industrial applications.

Morphological variation of siscowet lake trout in Lake Superior

USGS Publications Warehouse

Bronte, C.R.; Moore, S.A.

2007-01-01

Historically, Lake Superior has contained many morphologically distinct forms of the lake trout Salvelinus namaycush that have occupied specific depths and locations and spawned at specific times of the year. Today, as was probably the case historically, the siscowet morphotype is the most abundant. Recent interest in harvesting siscowets to extract oil containing omega-3 fatty acids will require additional knowledge of the biology and stock structure of these lightly exploited populations. The objective of this study was to determine whether shape differences exist among siscowet populations across Lake Superior and whether these shape differences can be used to infer stock structure. Morphometric analysis (truss protocol) was used to differentiate among siscowets sampled from 23 locations in Lake Superior. We analyzed 31 distance measurements among 14 anatomical landmarks taken from digital images of fish recorded in the field. Cluster analysis of size-corrected data separated fish into three geographic groups: The Isle Royale, eastern (Michigan), and western regions (Michigan). Finer scales of stock structure were also suggested. Discriminant function analysis demonstrated that head measurements contributed to most of the observed variation. Cross-validation classification rates indicated that 67–71% of individual fish were correctly classified to their region of capture. This is the first study to present shape differences associated with location within a lake trout morphotype in Lake Superior.

An Optimized Set of Fluorescence In Situ Hybridization Probes for Detection of Pancreatobiliary Tract Cancer in Cytology Brush Samples.

PubMed

Barr Fritcher, Emily G; Voss, Jesse S; Brankley, Shannon M; Campion, Michael B; Jenkins, Sarah M; Keeney, Matthew E; Henry, Michael R; Kerr, Sarah M; Chaiteerakij, Roongruedee; Pestova, Ekaterina V; Clayton, Amy C; Zhang, Jun; Roberts, Lewis R; Gores, Gregory J; Halling, Kevin C; Kipp, Benjamin R

2015-12-01

Pancreatobiliary cancer is detected by fluorescence in situ hybridization (FISH) of pancreatobiliary brush samples with UroVysion probes, originally designed to detect bladder cancer. We designed a set of new probes to detect pancreatobiliary cancer and compared its performance with that of UroVysion and routine cytology analysis. We tested a set of FISH probes on tumor tissues (cholangiocarcinoma or pancreatic carcinoma) and non-tumor tissues from 29 patients. We identified 4 probes that had high specificity for tumor vs non-tumor tissues; we called this set of probes pancreatobiliary FISH. We performed a retrospective analysis of brush samples from 272 patients who underwent endoscopic retrograde cholangiopancreatography for evaluation of malignancy at the Mayo Clinic; results were available from routine cytology and FISH with UroVysion probes. Archived residual specimens were retrieved and used to evaluate the pancreatobiliary FISH probes. Cutoff values for FISH with the pancreatobiliary probes were determined using 89 samples and validated in the remaining 183 samples. Clinical and pathologic evidence of malignancy in the pancreatobiliary tract within 2 years of brush sample collection was used as the standard; samples from patients without malignancies were used as negative controls. The validation cohort included 85 patients with malignancies (46.4%) and 114 patients with primary sclerosing cholangitis (62.3%). Samples containing cells above the cutoff for polysomy (copy number gain of ≥2 probes) were classified as positive in FISH with the UroVysion and pancreatobiliary probes. Multivariable logistic regression was used to estimate associations between clinical and pathology findings and results from FISH. The combination of FISH probes 1q21, 7p12, 8q24, and 9p21 identified cancer cells with 93% sensitivity and 100% specificity in pancreatobiliary tissue samples and were therefore included in the pancreatobiliary probe set. In the validation cohort of brush samples, pancreatobiliary FISH identified samples from patients with malignancy with a significantly higher level of sensitivity (64.7%) than the UroVysion probes (45.9%) (P < .001) or routine cytology analysis (18.8%) (P < .001), but similar specificity (92.9%, 90.8%, and 100.0% respectively). Factors significantly associated with detection of carcinoma, in adjusted analyses, included detection of polysomy by pancreatobiliary FISH (P < .001), a mass by cross-sectional imaging (P < .001), cancer cells by routine cytology (overall P = .003), as well as absence of primary sclerosing cholangitis (P = .011). We identified a set of FISH probes that detects cancer cells in pancreatobiliary brush samples from patients with and without primary sclerosing cholangitis with higher levels of sensitivity than UroVysion probes. Cytologic brushing test results and clinical features were independently associated with detection of cancer and might be used to identify patients with pancreatobiliary cancers. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Maximum-likelihood techniques for joint segmentation-classification of multispectral chromosome images.

PubMed

Schwartzkopf, Wade C; Bovik, Alan C; Evans, Brian L

2005-12-01

Traditional chromosome imaging has been limited to grayscale images, but recently a 5-fluorophore combinatorial labeling technique (M-FISH) was developed wherein each class of chromosomes binds with a different combination of fluorophores. This results in a multispectral image, where each class of chromosomes has distinct spectral components. In this paper, we develop new methods for automatic chromosome identification by exploiting the multispectral information in M-FISH chromosome images and by jointly performing chromosome segmentation and classification. We (1) develop a maximum-likelihood hypothesis test that uses multispectral information, together with conventional criteria, to select the best segmentation possibility; (2) use this likelihood function to combine chromosome segmentation and classification into a robust chromosome identification system; and (3) show that the proposed likelihood function can also be used as a reliable indicator of errors in segmentation, errors in classification, and chromosome anomalies, which can be indicators of radiation damage, cancer, and a wide variety of inherited diseases. We show that the proposed multispectral joint segmentation-classification method outperforms past grayscale segmentation methods when decomposing touching chromosomes. We also show that it outperforms past M-FISH classification techniques that do not use segmentation information.

Research on the feature set construction method for spherical stereo vision

NASA Astrophysics Data System (ADS)

Zhu, Junchao; Wan, Li; Röning, Juha; Feng, Weijia

2015-01-01

Spherical stereo vision is a kind of stereo vision system built by fish-eye lenses, which discussing the stereo algorithms conform to the spherical model. Epipolar geometry is the theory which describes the relationship of the two imaging plane in cameras for the stereo vision system based on perspective projection model. However, the epipolar in uncorrected fish-eye image will not be a line but an arc which intersects at the poles. It is polar curve. In this paper, the theory of nonlinear epipolar geometry will be explored and the method of nonlinear epipolar rectification will be proposed to eliminate the vertical parallax between two fish-eye images. Maximally Stable Extremal Region (MSER) utilizes grayscale as independent variables, and uses the local extremum of the area variation as the testing results. It is demonstrated in literatures that MSER is only depending on the gray variations of images, and not relating with local structural characteristics and resolution of image. Here, MSER will be combined with the nonlinear epipolar rectification method proposed in this paper. The intersection of the rectified epipolar and the corresponding MSER region is determined as the feature set of spherical stereo vision. Experiments show that this study achieved the expected results.

Miniaturized Embryo Array for Automated Trapping, Immobilization and Microperfusion of Zebrafish Embryos

PubMed Central

Akagi, Jin; Khoshmanesh, Khashayar; Evans, Barbara; Hall, Chris J.; Crosier, Kathryn E.; Cooper, Jonathan M.; Crosier, Philip S.; Wlodkowic, Donald

2012-01-01

Zebrafish (Danio rerio) has recently emerged as a powerful experimental model in drug discovery and environmental toxicology. Drug discovery screens performed on zebrafish embryos mirror with a high level of accuracy the tests usually performed on mammalian animal models, and fish embryo toxicity assay (FET) is one of the most promising alternative approaches to acute ecotoxicity testing with adult fish. Notwithstanding this, automated in-situ analysis of zebrafish embryos is still deeply in its infancy. This is mostly due to the inherent limitations of conventional techniques and the fact that metazoan organisms are not easily susceptible to laboratory automation. In this work, we describe the development of an innovative miniaturized chip-based device for the in-situ analysis of zebrafish embryos. We present evidence that automatic, hydrodynamic positioning, trapping and long-term immobilization of single embryos inside the microfluidic chips can be combined with time-lapse imaging to provide real-time developmental analysis. Our platform, fabricated using biocompatible polymer molding technology, enables rapid trapping of embryos in low shear stress zones, uniform drug microperfusion and high-resolution imaging without the need of manual embryo handling at various developmental stages. The device provides a highly controllable fluidic microenvironment and post-analysis eleuthero-embryo stage recovery. Throughout the incubation, the position of individual embryos is registered. Importantly, we also for first time show that microfluidic embryo array technology can be effectively used for the analysis of anti-angiogenic compounds using transgenic zebrafish line (fli1a:EGFP). The work provides a new rationale for rapid and automated manipulation and analysis of developing zebrafish embryos at a large scale. PMID:22606275

High-throughput behavioral screening method for detecting auditory response defects in zebrafish.

PubMed

Bang, Pascal I; Yelick, Pamela C; Malicki, Jarema J; Sewell, William F

2002-08-30

We have developed an automated, high-throughput behavioral screening method for detecting hearing defects in zebrafish. Our assay monitors a rapid escape reflex in response to a loud sound. With this approach, 36 adult zebrafish, restrained in visually isolated compartments, can be simultaneously assessed for responsiveness to near-field 400 Hz sinusoidal tone bursts. Automated, objective determinations of responses are achieved with a computer program that obtains images at precise times relative to the acoustic stimulus. Images taken with a CCD video camera before and after stimulus presentation are subtracted to reveal a response to the sound. Up to 108 fish can be screened per hour. Over 6500 fish were tested to validate the reliability of the assay. We found that 1% of these animals displayed hearing deficits. The phenotypes of non-responders were further assessed with radiological analysis for defects in the gross morphology of the auditory system. Nearly all of those showed abnormalities in conductive elements of the auditory system: the swim bladder or Weberian ossicles. Copyright 2002 Elsevier Science B.V.

Live-cell imaging combined with immunofluorescence, RNA, or DNA FISH to study the nuclear dynamics and expression of the X-inactivation center.

PubMed

Pollex, Tim; Piolot, Tristan; Heard, Edith

2013-01-01

Differentiation of embryonic stem cells is accompanied by changes of gene expression and chromatin and chromosome dynamics. One of the most impressive examples for these changes is inactivation of one of the two X chromosomes occurring upon differentiation of mouse female embryonic stem cells. With a few exceptions, these events have been mainly studied in fixed cells. In order to better understand the dynamics, kinetics, and order of events during differentiation, one needs to employ live-cell imaging techniques. Here, we describe a combination of live-cell imaging with techniques that can be used in fixed cells (e.g., RNA FISH) to correlate locus dynamics or subnuclear localization with, e.g., gene expression. To study locus dynamics in female ES cells, we generated cell lines containing TetO arrays in the X-inactivation center, the locus on the X chromosome regulating X-inactivation, which can be visualized upon expression of TetR fused to fluorescent proteins. We will use this system to elaborate on how to generate ES cell lines for live-cell imaging of locus dynamics, how to culture ES cells prior to live-cell imaging, and to describe typical live-cell imaging conditions for ES cells using different microscopes. Furthermore, we will explain how RNA, DNA FISH, or immunofluorescence can be applied following live-cell imaging to correlate gene expression with locus dynamics.

Specimen preparation, imaging, and analysis protocols for knife-edge scanning microscopy.

PubMed

Choe, Yoonsuck; Mayerich, David; Kwon, Jaerock; Miller, Daniel E; Sung, Chul; Chung, Ji Ryang; Huffman, Todd; Keyser, John; Abbott, Louise C

2011-12-09

Major advances in high-throughput, high-resolution, 3D microscopy techniques have enabled the acquisition of large volumes of neuroanatomical data at submicrometer resolution. One of the first such instruments producing whole-brain-scale data is the Knife-Edge Scanning Microscope (KESM), developed and hosted in the authors' lab. KESM has been used to section and image whole mouse brains at submicrometer resolution, revealing the intricate details of the neuronal networks (Golgi), vascular networks (India ink), and cell body distribution (Nissl). The use of KESM is not restricted to the mouse nor the brain. We have successfully imaged the octopus brain, mouse lung, and rat brain. We are currently working on whole zebra fish embryos. Data like these can greatly contribute to connectomics research; to microcirculation and hemodynamic research; and to stereology research by providing an exact ground-truth. In this article, we will describe the pipeline, including specimen preparation (fixing, staining, and embedding), KESM configuration and setup, sectioning and imaging with the KESM, image processing, data preparation, and data visualization and analysis. The emphasis will be on specimen preparation and visualization/analysis of obtained KESM data. We expect the detailed protocol presented in this article to help broaden the access to KESM and increase its utilization.

Earth Observation

NASA Image and Video Library

2014-07-27

ISS040-E-081424 (27 July 2014) --- From an altitude of 223 nautical miles, one of the Expedition 40 crew members aboard the International Space Station on July 27, 2014 recorded this oblique night image of Taiwan (center foreground) and part of mainland China. Hundreds of fishing vessels, perhaps for harvesting both fish and squid as well as other forms of marine life, are seen in clusters throughout the panorama. Two lightning storms -- one on either side of the image -- are also visible.

Conserving Shorebirds on Department of Defense Lands

DTIC Science & Technology

2007-06-01

Fish & Wildlife Service and the National Fish and Wildlife Foundation. The booklet also has benefited from advice of Chris Eberly (Department of...as noted, courtesy of U. S . Fish and Wildlife Service Digital Library System (http://images.fws.gov/) Whimbrel, page 5, courtesy of Richard...biologists have a unique opportunity to manage wetland and upland habitat in ways that benefit wildlife populations and help to reverse the rapid

Fish scale artefact on an intraoral imaging receptor.

PubMed

Buchanan, Allison; Morales, Carla; Looney, Stephen; Kalathingal, Sajitha

2017-12-01

To describe an artefact, termed the fish scale artefact, present on an intraoral imaging receptor. Thirty brand new DIGORA Optime photostimulable phosphor (PSP) plates (Soredex/Orion Corp., Helsinki, Finland) were imaged using the dental digital quality assurance radiographic phantom (Dental Imaging Consultants LLC, San Antonio, TX). All PSP plates were scanned at the same spatial resolution (dpi) using the high resolution mode. Two evaluators assessed all 30 plates. Each evaluator assessed the 30 PSP plates separately for purposes of establishing interrater reliability, and then together in order to obtain the gold standard result. The fish scale artefact was detected on 46.7% of the PSP plates. The kappa coefficient for interrater reliability was 0.86 [95% CI (0.69-1.00)], indicating excellent interrater reliability. For Evaluator 1, sensitivity was 0.85 [95% CI (0.55-0.98)]; specificity was 0.94 [CI (0.71-1.00)] and overall accuracy was 0.90 [95% CI (0.73-0.98)]. For Evaluator 2, sensitivity was 1.00 [95% CI (0.75-1.00)]; specificity was 0.94 [CI (0.71-1.00)] and overall accuracy was 0.97 [95% CI (0.83-1.00)]. These results indicate excellent agreement with the gold standard for both evaluators. Utilizing a comprehensive quality assurance protocol, we identified a fish scale artefact inherent to the image receptor. Additional research is needed to determine if the artefact remains static over time or if it increases over time. Likewise, research to determine the potential sources contributing to an increase in the artefact is needed.

Vibrios from Fish Pen Slime Which Mimic Escherichia coli on Violet Red Bile Agar

PubMed Central

Rosen, A.; Levin, R. E.

1970-01-01

Organisms from fish pen slime which mimicked coliforms and Escherichia coli on Violet Red Bile Agar were identified as members of the genus Vibrio on the basis of metabolic and morphological characteristics. Images PMID:4195607

Automatic identification of species with neural networks.

PubMed

Hernández-Serna, Andrés; Jiménez-Segura, Luz Fernanda

2014-01-01

A new automatic identification system using photographic images has been designed to recognize fish, plant, and butterfly species from Europe and South America. The automatic classification system integrates multiple image processing tools to extract the geometry, morphology, and texture of the images. Artificial neural networks (ANNs) were used as the pattern recognition method. We tested a data set that included 740 species and 11,198 individuals. Our results show that the system performed with high accuracy, reaching 91.65% of true positive fish identifications, 92.87% of plants and 93.25% of butterflies. Our results highlight how the neural networks are complementary to species identification.

Observation of Accumulated Metal Cation Distribution in Fish by Novel Stigmatic Imaging Time-of-Flight Mass Spectrometer

NASA Astrophysics Data System (ADS)

Aoki, Jun; Ikeda, Shinichiro; Toyoda, Michisato

2014-02-01

The accumulation of radioactive substances in biological organisms is a matter of great concern since the incident at the nuclear power plant in Fukushima, Japan. We have developed a novel technique for observing the distribution of accumulated metal cations in fish that employs a new imaging mass spectrometer, MULTUM-IMG2. Distributions of 133Cs and 88Sr in a sliced section of medaka (Oryzias latipes) are obtained with spatial resolution of µm-scale.

Measuring mRNA copy-number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization (smFISH)

PubMed Central

Skinner, Samuel O.; Sepúlveda, Leonardo A.; Xu, Heng; Golding, Ido

2014-01-01

We present a method for measuring the absolute number of mRNA molecules from a gene of interest in individual, chemically fixed Escherichia coli cells. A set of fluorescently-labeled oligonucleotide probes are hybridized to the target mRNA, so that each mRNA molecule is decorated by a known number of fluorescent dyes. Cells are then imaged using fluorescence microscopy. The number of target mRNA is estimated from the total intensity of fluorescent foci in the cell, rather than from counting discrete “spots” as in other currently available protocols. Image analysis is performed using an automated algorithm. The measured mRNA copy-number distribution obtained from many individual cells can be used to extract the parameters of stochastic gene activity, namely the frequency and size of transcription bursts from the gene of interest. The experimental procedure takes 2 days, with another 2-3 days typically required for image and data analysis. PMID:23680982

The use of fish models to study human neurological disorders.

PubMed

Matsui, Hideaki

2017-07-01

Small teleost fish including zebrafish and medaka have been used as animal models in basic science research due to the relative ease of handling and transparency during embryogenesis. Current advances in genetic engineering and progress in disease genetics allowed utilization of these fish to study neurological diseases and psychiatric disorders. This review summarizes the advantages and disadvantages of using fish for neuropsychiatric research using primarily our own studies as examples. We discuss how fish belong to a class of vertebrates, are feasible for imaging, and include diverse species with multiple research possibilities yet to be discovered. Copyright © 2017 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

Comparison of conventional culture method and fluorescent in situ hybridization technique for detection of Listeria spp. in ground beef, turkey, and chicken breast fillets in İzmir, Turkey.

PubMed

Baysal, Ayse Handan

2014-12-01

The occurrence of Listeria species in refrigerated fresh chicken breast fillet, turkey breast fillet, and ground beef was evaluated, comparing the conventional culture method and fluorescent in situ hybridization (FISH). FISH uses hybridization of a nucleic acid sequence target of a microorganism with a specific DNA probe labeled with a fluorochrome and imaging by a fluorescence microscope. First, Listeria was inoculated in chicken breast fillet, turkey breast fillet, or ground beef, and the applicability of the FISH method was evaluated. Second, Listeria was detected in fresh chicken breast fillet, turkey breast fillet, and ground beef by culture and FISH methods. Listeria was isolated from 27 (37.4%) of 216 samples by the standard culture method, whereas FISH detected 25 (24.7%) preenriched samples. Of these isolates, 17 (63%) were L. innocua, 6 (22%) L. welshimeri, and 4 (14.8%) L. seeligeri. Overall, the prevalences of Listeria spp. found with the conventional culture method in chicken breast fillet, turkey breast fillet, and ground beef were 9.7, 6.9, and 20.8%, whereas with the FISH technique these values were 11.1, 6.9, and 16.7%, respectively. The molecular FISH technique appears to be a cheap, sensitive, and time-efficient procedure that could be used for routine detection of Listeria spp. in meat. This study showed that retail raw meats are potentially contaminated with Listeria spp. and are, thus, vehicles for transmitting diseases caused by foodborne pathogens, underlining the need for increased precautions, such as implementation of hazard analysis and critical control points and consumer food safety education.

Evaluation of the microscopic distribution of florfenicol in feed pellets for salmon by Fourier Transform infrared imaging and multivariate analysis.

PubMed

Bastidas, Camila Y; von Plessing, Carlos; Troncoso, José; Del P Castillo, Rosario

2018-04-15

Fourier Transform infrared imaging and multivariate analysis were used to identify, at the microscopic level, the presence of florfenicol (FF), a heavily-used antibiotic in the salmon industry, supplied to fishes in feed pellets for the treatment of salmonid rickettsial septicemia (SRS). The FF distribution was evaluated using Principal Component Analysis (PCA) and Augmented Multivariate Curve Resolution with Alternating Least Squares (augmented MCR-ALS) on the spectra obtained from images with pixel sizes of 6.25 μm × 6.25 μm and 1.56 μm × 1.56 μm, in different zones of feed pellets. Since the concentration of the drug was 3.44 mg FF/g pellet, this is the first report showing the powerful ability of the used of spectroscopic techniques and multivariate analysis, especially the augmented MCR-ALS, to describe the FF distribution in both the surface and inner parts of feed pellets at low concentration, in a complex matrix and at the microscopic level. The results allow monitoring the incorporation of the drug into the feed pellets. Copyright © 2018 Elsevier B.V. All rights reserved.

View of the Cupola RWS taken with Fish-Eye Lens

NASA Image and Video Library

2010-05-08

ISS023-E-039983 (8 May 2010) --- A fish-eye lens attached to an electronic still camera was used by an Expedition 23 crew member to capture this image of the robotic workstation in the Cupola of the International Space Station.

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

PubMed

Sato, Yukuto; Miya, Masaki; Fukunaga, Tsukasa; Sado, Tetsuya; Iwasaki, Wataru

2018-06-01

Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed April 7th, 2018).

Ciguatera fish poisoning. A southern California epidemic.

PubMed Central

Barton, E D; Tanner, P; Turchen, S G; Tunget, C L; Manoguerra, A; Clark, R F

1995-01-01

Ciguatera fish poisoning results from the bioconcentration of a variety of toxins produced by marine dinoflagellates. Signs and symptoms vary widely, but it usually presents as gastrointestinal and neurologic complaints beginning shortly after the ingestion of fish containing the toxins. Symptoms may persist for months and sometimes even years. Although cases have been reported throughout the United States, epidemics are most common along tropical and subtropical coasts and usually involve the ingestion of large carnivorous fish. We review the literature and report the first epidemic of 25 cases of ciguatera fish poisoning presenting to area hospitals in Southern California that were successfully tracked by the Department of Health Services and isolated to fish caught off the coast of Baja California, Mexico. Images Figure 1. PMID:7667980

Acute transcriptional up-regulation specific to osteoblasts/osteoclasts in medaka fish immediately after exposure to microgravity

PubMed Central

Chatani, Masahiro; Morimoto, Hiroya; Takeyama, Kazuhiro; Mantoku, Akiko; Tanigawa, Naoki; Kubota, Koji; Suzuki, Hiromi; Uchida, Satoko; Tanigaki, Fumiaki; Shirakawa, Masaki; Gusev, Oleg; Sychev, Vladimir; Takano, Yoshiro; Itoh, Takehiko; Kudo, Akira

2016-01-01

Bone loss is a serious problem in spaceflight; however, the initial action of microgravity has not been identified. To examine this action, we performed live-imaging of animals during a space mission followed by transcriptome analysis using medaka transgenic lines expressing osteoblast and osteoclast-specific promoter-driven GFP and DsRed. In live-imaging for osteoblasts, the intensity of osterix- or osteocalcin-DsRed fluorescence in pharyngeal bones was significantly enhanced 1 day after launch; and this enhancement continued for 8 or 5 days. In osteoclasts, the signals of TRAP-GFP and MMP9-DsRed were highly increased at days 4 and 6 after launch in flight. HiSeq from pharyngeal bones of juvenile fish at day 2 after launch showed up-regulation of 2 osteoblast- and 3 osteoclast- related genes. Gene ontology analysis for the whole-body showed that transcription of genes in the category “nucleus” was significantly enhanced; particularly, transcription-regulators were more up-regulated at day 2 than at day 6. Lastly, we identified 5 genes, c-fos, jun-B-like, pai-1, ddit4 and tsc22d3, which were up-regulated commonly in the whole-body at days 2 and 6, and in the pharyngeal bone at day 2. Our results suggested that exposure to microgravity immediately induced dynamic alteration of gene expression levels in osteoblasts and osteoclasts. PMID:28004797

Validation of a new classifier for the automated analysis of the human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer specimens

PubMed Central

2013-01-01

Amplification of the human epidermal growth factor receptor 2 (HER2) is a prognostic marker for poor clinical outcome and a predictive marker for therapeutic response to targeted therapies in breast cancer patients. With the introduction of anti-HER2 therapies, accurate assessment of HER2 status has become essential. Fluorescence in situ hybridization (FISH) is a widely used technique for the determination of HER2 status in breast cancer. However, the manual signal enumeration is time-consuming. Therefore, several companies like MetaSystem have developed automated image analysis software. Some of these signal enumeration software employ the so called “tile-sampling classifier”, a programming algorithm through which the software quantifies fluorescent signals in images on the basis of square tiles of fixed dimensions. Considering that the size of tile does not always correspond to the size of a single tumor cell nucleus, some users argue that this analysis method might not completely reflect the biology of cells. For that reason, MetaSystems has developed a new classifier which is able to recognize nuclei within tissue sections in order to determine the HER2 amplification status on nuclei basis. We call this new programming algorithm “nuclei-sampling classifier”. In this study, we evaluated the accuracy of the “nuclei-sampling classifier” in determining HER2 gene amplification by FISH in nuclei of breast cancer cells. To this aim, we randomly selected from our cohort 64 breast cancer specimens (32 nonamplified and 32 amplified) and we compared results obtained through manual scoring and through this new classifier. The new classifier automatically recognized individual nuclei. The automated analysis was followed by an optional human correction, during which the user interacted with the software in order to improve the selection of cell nuclei automatically selected. Overall concordance between manual scoring and automated nuclei-sampling analysis was 98.4% (100% for nonamplified cases and 96.9% for amplified cases). However, after human correction, concordance between the two methods was 100%. We conclude that the nuclei-based classifier is a new available tool for automated quantitative HER2 FISH signals analysis in nuclei in breast cancer specimen and it can be used for clinical purposes. PMID:23379971

Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots.

PubMed

Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

2018-07-13

Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores' blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

2018-07-01

Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores’ blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

An automated approach to improve efficacy in detecting residual malignant cancer cell for facilitating prognostic assessment of leukemia: an initial study

NASA Astrophysics Data System (ADS)

Qiu, Yuchen; Lu, Xianglan; Tan, Maxine; Li, Shibo; Liu, Hong; Zheng, Bin

2015-03-01

The purpose of this study is to investigate the feasibility of applying automatic interphase FISH cells analysis method for detecting the residual malignancy of post chemotherapy leukemia patients. In the experiment, two clinical specimens with translocation between chromosome No. 9 and 22 or No. 11 and 14 were selected from the patients underwent leukemia diagnosis and treatment. The entire slide of each specimen was first digitalized by a commercial fluorescent microscope using a 40× objective lens. Then, the scanned images were processed by a computer-aided detecting (CAD) scheme to identify the analyzable FISH cells, which is accomplished by applying a series of features including the region size, Brenner gradient and maximum intensity. For each identified cell, the scheme detected and counted the number of the FISH signal dots inside the nucleus, using the adaptive threshold of the region size and distance of the labeled FISH dots. The results showed that the new CAD scheme detected 8093 and 6675 suspicious regions of interest (ROI) in two specimens, among which 4546 and 3807 ROI contain analyzable interphase FISH cell. In these analyzable ROIs, CAD selected 334 and 405 residual malignant cancer cells, which is substantially more than those visually detected in a cytogenetic laboratory of our medical center (334 vs. 122, 405 vs. 160). This investigation indicates that an automatic interphase FISH cell scanning and CAD method has the potential to improve the accuracy and efficiency of the prognostic assessment for leukemia and other genetic related cancer patients in the future.

Fish embryo toxicity test: identification of compounds with weak toxicity and analysis of behavioral effects to improve prediction of acute toxicity for neurotoxic compounds.

PubMed

Klüver, Nils; König, Maria; Ortmann, Julia; Massei, Riccardo; Paschke, Albrecht; Kühne, Ralph; Scholz, Stefan

2015-06-02

The fish embryo toxicity test has been proposed as an alternative for the acute fish toxicity test, but concerns have been raised for its predictivity given that a few compounds have been shown to exhibit a weak acute toxicity in the fish embryo. In order to better define the applicability domain and improve the predictive capacity of the fish embryo test, we performed a systematic analysis of existing fish embryo and acute fish toxicity data. A correlation analysis of a total of 153 compounds identified 28 compounds with a weaker or no toxicity in the fish embryo test. Eleven of these compounds exhibited a neurotoxic mode of action. We selected a subset of eight compounds with weaker or no embryo toxicity (cyanazine, picloram, aldicarb, azinphos-methyl, dieldrin, diquat dibromide, endosulfan, and esfenvalerate) to study toxicokinetics and a neurotoxic mode of action as potential reasons for the deviating fish embryo toxicity. Published fish embryo LC50 values were confirmed by experimental analysis of zebrafish embryo LC50 according to OECD guideline 236. Except for diquat dibromide, internal concentration analysis did not indicate a potential relation of the low sensitivity of fish embryos to a limited uptake of the compounds. Analysis of locomotor activity of diquat dibromide and the neurotoxic compounds in 98 hpf embryos (exposed for 96 h) indicated a specific effect on behavior (embryonic movement) for the neurotoxic compounds. The EC50s of behavior for neurotoxic compounds were close to the acute fish toxicity LC50. Our data provided the first evidence that the applicability domain of the fish embryo test (LC50s determination) may exclude neurotoxic compounds. However, neurotoxic compounds could be identified by changes in embryonic locomotion. Although a quantitative prediction of acute fish toxicity LC50 using behavioral assays in fish embryos may not yet be possible, the identification of neurotoxicity could trigger the conduction of a conventional fish acute toxicity test or application of assessment factors while considering the very good fish embryo-acute fish toxicity correlation for other compounds.

Estimation of leaf area index using WorldView-2 and Aster satellite image: a case study from Turkey.

PubMed

Günlü, Alkan; Keleş, Sedat; Ercanlı, İlker; Şenyurt, Muammer

2017-10-04

The objective of this study is to estimate the leaf area index (LAI) of a forest ecosystem using two different satellite images, WorldView-2 and Aster. For this purpose, 108 sample plots were taken from pure Crimean pine forest stands of Yenice Forest Management Planning Unit in Ilgaz Forest Management Enterprise, Turkey. Each sample plot was imaged with hemispherical photographs with a fish-eye camera to determine the LAI. These photographs were analyzed with the help of Hemisfer Hemiview software program, and thus, the LAI of each sample plot was estimated. Furthermore, multiple regression analysis method was used to model the statistical relationships between the LAI values and band spectral reflection values and some vegetation indices (Vis) obtained from satellite images. The results show that the high-resolution WorldView-2 satellite image is better than the medium-resolution Aster satellite image in predicting the LAI. It was also seen that the results obtained by using the VIs are better than the bands when the LAI value is predicted with satellite images.

Suitability of hyperspectral imaging for rapid evaluation of thiobarbituric acid (TBA) value in grass carp (Ctenopharyngodon idella) fillet.

PubMed

Cheng, Jun-Hu; Sun, Da-Wen; Pu, Hong-Bin; Wang, Qi-Jun; Chen, Yu-Nan

2015-03-15

The suitability of hyperspectral imaging technique (400-1000 nm) was investigated to determine the thiobarbituric acid (TBA) value for monitoring lipid oxidation in fish fillets during cold storage at 4°C for 0, 2, 5, and 8 days. The PLSR calibration model was established with full spectral region between the spectral data extracted from the hyperspectral images and the reference TBA values and showed good performance for predicting TBA value with determination coefficients (R(2)P) of 0.8325 and root-mean-square errors of prediction (RMSEP) of 0.1172 mg MDA/kg flesh. Two simplified PLSR and MLR models were built and compared using the selected ten most important wavelengths. The optimised MLR model yielded satisfactory results with R(2)P of 0.8395 and RMSEP of 0.1147 mg MDA/kg flesh, which was used to visualise the TBA values distribution in fish fillets. The whole results confirmed that using hyperspectral imaging technique as a rapid and non-destructive tool is suitable for the determination of TBA values for monitoring lipid oxidation and evaluation of fish freshness. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the hydrodynamics of archer fish jumping out of the water: Integrating experiments with numerical simulations

NASA Astrophysics Data System (ADS)

Sotiropoulos, Fotis; Angelidis, Dionysios; Mendelson, Leah; Techet, Alexandra

2017-11-01

Evolution has enabled fish to develop a range of thrust producing mechanisms to allow skillful movement and give them the ability to catch prey or avoid danger. Several experimental and numerical studies have been performed to investigate how complex maneuvers are executed and develop bioinspired strategies for aquatic robot design. We will discuss recent numerical advances toward the development of a computational framework for performing turbulent, two-phase flow, fluid-structure-interaction (FSI) simulations to investigate the dynamics of aquatic jumpers. We will also discuss the integration of such numerics with high-speed imaging and particle image velocimetry data to reconstruct anatomic fish models and prescribe realistic kinematics of fish motion. The capabilities of our method will be illustrated by applying it to simulate the motion of a small scale archer fish jumping out of the water to capture prey. We will discuss the rich vortex dynamics emerging during the hovering, rapid upward and gliding phases. The simulations will elucidate the thrust production mechanisms by the movement of the pectoral and anal fins and we will show that the fins significantly contribute to the rapid acceleration.

Laser Scanning Cytometry: Principles and Applications—An Update

PubMed Central

Pozarowski, Piotr; Holden, Elena; Darzynkiewicz, Zbigniew

2012-01-01

Laser scanning cytometer (LSC) is the microscope-based cytofluorometer that offers a plethora of unique analytical capabilities, not provided by flow cytometry (FCM). This review describes attributes of LSC and covers its numerous applications derived from plentitude of the parameters that can be measured. Among many LSC applications the following are emphasized: (a) assessment of chromatin condensation to identify mitotic, apoptotic cells, or senescent cells; (b) detection of nuclear or mitochondrial translocation of critical factors such as NF-κB, p53, or Bax; (c) semi-automatic scoring of micronuclei in mutagenicity assays; (d) analysis of fluorescence in situ hybridization (FISH) and use of the FISH analysis attribute to measure other punctuate fluorescence patterns such as γH2AX foci or receptor clustering; (e) enumeration and morphometry of nucleoli and other cell organelles; (f) analysis of progeny of individual cells in clonogenicity assay; (g) cell immunophenotyping; (h) imaging, visual examination, or sequential analysis using different probes of the same cells upon their relocation; (i) in situ enzyme kinetics, drug uptake, and other time-resolved processes; (j) analysis of tissue section architecture using fluorescent and chromogenic probes; (k) application for hypocellular samples (needle aspirate, spinal fluid, etc.); and (l) other clinical applications. Advantages and limitations of LSC are discussed and compared with FCM. PMID:23027005

Theory of Maxwell's fish eye with mutually interacting sources and drains

NASA Astrophysics Data System (ADS)

Leonhardt, Ulf; Sahebdivan, Sahar

2015-11-01

Maxwell's fish eye is predicted to image with a resolution not limited by the wavelength of light. However, interactions between sources and drains may ruin the subwavelength imaging capabilities of this and similar absolute optical instruments. Nevertheless, as we show in this paper, at resonance frequencies of the device, an array of drains may resolve a single source, or alternatively, a single drain may scan an array of sources, no matter how narrowly spaced they are. It seems that near-field information can be obtained from far-field distances.

Motion reconstruction of animal groups: From schooling fish to swarming mosquitoes

NASA Astrophysics Data System (ADS)

Butail, Sachit

The long-term goal of this research is to provide kinematic data for the design and validation of spatial models of collective behavior in animal groups. The specific research objective of this dissertation is to apply methods from nonlinear estimation and computer vision to construct multi-target tracking systems that process multi-view calibrated video to reconstruct the three-dimensional movement of animals in a group. We adapt the tracking systems for the study of two animal species: Danio aequipinnatus, a common species of schooling fish, and Anopheles gambiae, the most important vector of malaria in sub-Saharan Africa. Together these tracking systems span variability in target size on image, density, and movement. For tracking fish, we automatically initialize, predict, and reconstruct shape trajectories of multiple fish through occlusions. For mosquitoes, which appear as faded streaks on in-field footage, we provide methods to extract velocity information from the streaks, adaptively seek missing measurements, and resolve occlusions within a multi-hypothesis framework. In each case the research has yielded an unprecedented volume of trajectory data for subsequent analysis. We present kinematic data of fast-start response in fish schools and first-ever trajectories of wild mosquito swarming and mating events. The broader impact of this work is to advance the understanding of animal groups for the design of bio-inspired robotic systems, where, similar to the animal groups we study, the collective is able to perform tasks far beyond the capabilities of a single inexpensive robot.

Fish-Eye Observing with Phased Array Radio Telescopes

NASA Astrophysics Data System (ADS)

Wijnholds, S. J.

The radio astronomical community is currently developing and building several new radio telescopes based on phased array technology. These telescopes provide a large field-of-view, that may in principle span a full hemisphere. This makes calibration and imaging very challenging tasks due to the complex source structures and direction dependent radio wave propagation effects. In this thesis, calibration and imaging methods are developed based on least squares estimation of instrument and source parameters. Monte Carlo simulations and actual observations with several prototype show that this model based approach provides statistically and computationally efficient solutions. The error analysis provides a rigorous mathematical framework to assess the imaging performance of current and future radio telescopes in terms of the effective noise, which is the combined effect of propagated calibration errors, noise in the data and source confusion.

Predicting the Distribution of Yellowfin Tuna in Philippine Waters

NASA Astrophysics Data System (ADS)

Perez, G. J. P.; Leonardo, E. M.

2015-12-01

The Philippines is considered as a major tuna producer in the Western and Central Pacific Ocean, both for domestic consumption and on industrial scale. However, with the ever-increasing demand of growing population, it has always been a challenge to achieve sustainable fishing. The creation of satellite-derived potential fishing zone maps is a technology that has been adopted by advanced countries for almost three decades already and has led to reduction in search times by up to 40%. In this study, a Generalized Additive Model (GAM) is developed to predict the distribution of the Yellowfin tuna species in seas surrounding the Philippines based on the Catch-Per-Unit-Effort (CPUE) index. Level 3 gridded chlorophyll-a and sea surface temperature from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Aqua satellite of the National Aeronautics and Space Administration (NASA) are the main input parameters of the model. Chlorophyll-a is linked with the presence of phytoplankton, which indicates primary productivity and suggests potential regions of fish aggregation. Fish also prefers to stay in regions where the temperature is stable, thus the sea surface temperature fronts serve as a guide to locate concentrations of fish school. Historical monthly tuna catch data from Western and Central Pacific Commissions (WCPFC) is used to train the model. The resulting predictions are converted to potential fishing zone maps and are evaluated within and beyond the historical time range of the training data used. Diagnostic tests involving adjusted R2 value, GAM residual plots and root mean square error value are used to assess the accuracy of the model. The generated maps were able to confirm locations of known tuna fishing grounds in Mindanao and other parts of the country, as well us detect their seasonality and interannual variability. To improve the performance of the model, ancillary data such as surface winds reanalysis from National Centers for Environmental Prediction (NCEP) is also incorporated in the model. Results of the model are further analyzed by comparing the fish maps with the night fishing activities in the Philippine waters. This was done through the use of night light monthly images gathered by Visible Infrared Imaging Radiometer Suite (VIIRS) within the Philippine Exclusive Economic Zone (EEZ).

Quantification of red myotomal muscle volume and geometry in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis) using T1-weighted magnetic resonance imaging.

PubMed

Perry, Cameron N; Cartamil, Daniel P; Bernal, Diego; Sepulveda, Chugey A; Theilmann, Rebecca J; Graham, Jeffrey B; Frank, Lawrence R

2007-04-01

T1-weighted magnetic resonance imaging (MRI) in conjunction with image and segmentation analysis (i.e., the process of digitally partitioning tissues based on specified MR image characteristics) was evaluated as a noninvasive alternative for differentiating muscle fiber types and quantifying the amounts of slow, red aerobic muscle in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis). MRI-determinations of red muscle quantity and position made for the mid-body sections of three mako sharks (73.5-110 cm fork length, FL) are in close agreement (within the 95% confidence intervals) with data obtained for the same sections by the conventional dissection method involving serial cross-sectioning and volumetric analyses, and with previously reported findings for this species. The overall distribution of salmon shark red muscle as a function of body fork length was also found to be consistent with previously acquired serial dissection data for this species; however, MR imaging revealed an anterior shift in peak red muscle cross-sectional area corresponding to an increase in body mass. Moreover, MRI facilitated visualization of the intact and anatomically correct relationship of tendon linking the red muscle and the caudal peduncle. This study thus demonstrates that MRI is effective in acquiring high-resolution three-dimensional digital data with high contrast between different fish tissue types. Relative to serial dissection, MRI allows more precise quantification of the position, volume, and other details about the types of muscle within the fish myotome, while conserving specimen structural integrity. Copyright (c) 2007 Wiley-Liss, Inc.

USE OF MULTIPHOTON LASER SCANNING MICROSCOPY TO IMAGE BENZO[A]PYRENE AND METABOLITES IN FISH EGGS

EPA Science Inventory

Multiphoton laser scanning microscopy (MPLSM) is a promising tool to study the tissue distribution of environmental chemical contaminants during fish early life stages. One such chemical for which this is possible is benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon that a...

Pursuit and prediction in the tracking of moving food by a teleost fish (Acanthaluteres spilomelanurus).

PubMed

Lanchester, B S; Mark, R F

1975-12-01

1. The path, eye and body movements of a teleost fish (the leatherjacket Acanthaluteres spilomelanurus) approaching and taking food were measured by cinematography. 2. Fixation of the food by movement of the eyes is an invariable feature of the approach. The eyes then remain aligned with the target while the body moves forward and round to bring the mouth to the food. 3. When pursuing pieces of food moving vertically at constant velocity through the water these fish normally trace out the pathway that can be calculated by assuming the fish aims constantly at the food. Predictive pathways that imply anticipation of the point of intersection with the food are not regularly seen. 4. Deviations from pursuit occur sporadically, usually in the direction of a predictive path, particularly when the fish approach falling food from below. 5. The geometry of the situation suggests that predictive paths may sometimes be generated if the alignment of eye and body during the pursuit of moving food can be delayed. In approaches from below this may be because forward movement of the fish would tend to stabilize the image of the falling food in the retina. 6. We suggest that a simple linked control system using both eye and body movements to fixate retinal images will on occasions generate predictive pathways without any need for the central nervous system to calculate them in advance.

A Comparative Study of Vertebrate Corneal Structure: The Evolution of a Refractive Lens

PubMed Central

Winkler, Moritz; Shoa, Golroxan; Tran, Stephanie T.; Xie, Yilu; Thomasy, Sarah; Raghunathan, Vijay K.; Murphy, Christopher; Brown, Donald J.; Jester, James V.

2015-01-01

Purpose. Although corneal curvature plays an important role in determining the refractive power of the vertebrate eye, the mechanisms controlling corneal shape remain largely unknown. To address this question, we performed a comparative study of vertebrate corneal structure to identify potential evolutionarily based changes that correlate with the development of a corneal refractive lens. Methods. Nonlinear optical (NLO) imaging of second-harmonic–generated (SHG) signals was used to image collagen and three-dimensionally reconstruct the lamellar organization in corneas from different vertebrate clades. Results. Second-harmonic–generated images taken normal to the corneal surface showed that corneal collagen in all nonmammalian vertebrates was organized into sheets (fish and amphibians) or ribbons (reptiles and birds) extending from limbus to limbus that were oriented nearly orthogonal (ranging from 77.7°–88.2°) to their neighbors. The slight angular offset (2°–13°) created a rotational pattern that continued throughout the full thickness in fish and amphibians and to the very posterior layers in reptiles and birds. Interactions between lamellae were limited to “sutural” fibers in cartilaginous fish, and occasional lamellar branching in fish and amphibians. There was a marked increase in lamellar branching in higher vertebrates, such that birds ≫ reptiles > amphibians > fish. By contrast, mammalian corneas showed a nearly random collagen fiber organization with no orthogonal, chiral pattern. Conclusions. Our data indicate that nonmammalian vertebrate corneas share a common orthogonal collagen structural organization that shows increased lamellar branching in higher vertebrate species. Importantly, mammalian corneas showed a different structural organization, suggesting a divergent evolutionary background. PMID:26066606

A Comparative Study of Vertebrate Corneal Structure: The Evolution of a Refractive Lens.

PubMed

Winkler, Moritz; Shoa, Golroxan; Tran, Stephanie T; Xie, Yilu; Thomasy, Sarah; Raghunathan, Vijay K; Murphy, Christopher; Brown, Donald J; Jester, James V

2015-04-01

Although corneal curvature plays an important role in determining the refractive power of the vertebrate eye, the mechanisms controlling corneal shape remain largely unknown. To address this question, we performed a comparative study of vertebrate corneal structure to identify potential evolutionarily based changes that correlate with the development of a corneal refractive lens. Nonlinear optical (NLO) imaging of second-harmonic-generated (SHG) signals was used to image collagen and three-dimensionally reconstruct the lamellar organization in corneas from different vertebrate clades. Second-harmonic-generated images taken normal to the corneal surface showed that corneal collagen in all nonmammalian vertebrates was organized into sheets (fish and amphibians) or ribbons (reptiles and birds) extending from limbus to limbus that were oriented nearly orthogonal (ranging from 77.7°-88.2°) to their neighbors. The slight angular offset (2°-13°) created a rotational pattern that continued throughout the full thickness in fish and amphibians and to the very posterior layers in reptiles and birds. Interactions between lamellae were limited to "sutural" fibers in cartilaginous fish, and occasional lamellar branching in fish and amphibians. There was a marked increase in lamellar branching in higher vertebrates, such that birds ≫ reptiles > amphibians > fish. By contrast, mammalian corneas showed a nearly random collagen fiber organization with no orthogonal, chiral pattern. Our data indicate that nonmammalian vertebrate corneas share a common orthogonal collagen structural organization that shows increased lamellar branching in higher vertebrate species. Importantly, mammalian corneas showed a different structural organization, suggesting a divergent evolutionary background.

Detecting the presence-absence of bluefin tuna by automated analysis of medium-range sonars on fishing vessels.

PubMed

Uranga, Jon; Arrizabalaga, Haritz; Boyra, Guillermo; Hernandez, Maria Carmen; Goñi, Nicolas; Arregui, Igor; Fernandes, Jose A; Yurramendi, Yosu; Santiago, Josu

2017-01-01

This study presents a methodology for the automated analysis of commercial medium-range sonar signals for detecting presence/absence of bluefin tuna (Tunnus thynnus) in the Bay of Biscay. The approach uses image processing techniques to analyze sonar screenshots. For each sonar image we extracted measurable regions and analyzed their characteristics. Scientific data was used to classify each region into a class ("tuna" or "no-tuna") and build a dataset to train and evaluate classification models by using supervised learning. The methodology performed well when validated with commercial sonar screenshots, and has the potential to automatically analyze high volumes of data at a low cost. This represents a first milestone towards the development of acoustic, fishery-independent indices of abundance for bluefin tuna in the Bay of Biscay. Future research lines and additional alternatives to inform stock assessments are also discussed.

Detecting the presence-absence of bluefin tuna by automated analysis of medium-range sonars on fishing vessels

PubMed Central

Uranga, Jon; Arrizabalaga, Haritz; Boyra, Guillermo; Hernandez, Maria Carmen; Goñi, Nicolas; Arregui, Igor; Fernandes, Jose A.; Yurramendi, Yosu; Santiago, Josu

2017-01-01

This study presents a methodology for the automated analysis of commercial medium-range sonar signals for detecting presence/absence of bluefin tuna (Tunnus thynnus) in the Bay of Biscay. The approach uses image processing techniques to analyze sonar screenshots. For each sonar image we extracted measurable regions and analyzed their characteristics. Scientific data was used to classify each region into a class (“tuna” or “no-tuna”) and build a dataset to train and evaluate classification models by using supervised learning. The methodology performed well when validated with commercial sonar screenshots, and has the potential to automatically analyze high volumes of data at a low cost. This represents a first milestone towards the development of acoustic, fishery-independent indices of abundance for bluefin tuna in the Bay of Biscay. Future research lines and additional alternatives to inform stock assessments are also discussed. PMID:28152032

High-throughput imaging of adult fluorescent zebrafish with an LED fluorescence macroscope

PubMed Central

Blackburn, Jessica S; Liu, Sali; Raimondi, Aubrey R; Ignatius, Myron S; Salthouse, Christopher D; Langenau, David M

2011-01-01

Zebrafish are a useful vertebrate model for the study of development, behavior, disease and cancer. A major advantage of zebrafish is that large numbers of animals can be economically used for experimentation; however, high-throughput methods for imaging live adult zebrafish had not been developed. Here, we describe protocols for building a light-emitting diode (LED) fluorescence macroscope and for using it to simultaneously image up to 30 adult animals that transgenically express a fluorescent protein, are transplanted with fluorescently labeled tumor cells or are tagged with fluorescent elastomers. These protocols show that the LED fluorescence macroscope is capable of distinguishing five fluorescent proteins and can image unanesthetized swimming adult zebrafish in multiple fluorescent channels simultaneously. The macroscope can be built and used for imaging within 1 day, whereas creating fluorescently labeled adult zebrafish requires 1 hour to several months, depending on the method chosen. The LED fluorescence macroscope provides a low-cost, high-throughput method to rapidly screen adult fluorescent zebrafish and it will be useful for imaging transgenic animals, screening for tumor engraftment, and tagging individual fish for long-term analysis. PMID:21293462

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf

Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failedmore » to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.« less

Losing focus: how lens position and viewing angle affect the function of multifocal lenses in fishes.

PubMed

Gagnon, Yakir Luc; Wilby, David; Temple, Shelby Eric

2016-09-01

Light rays of different wavelengths are focused at different distances when they pass through a lens (longitudinal chromatic aberration [LCA]). For animals with color vision this can pose a serious problem, because in order to perceive a sharp image the rays must be focused at the shallow plane of the photoreceptor's outer segments in the retina. A variety of fish and tetrapods have been found to possess multifocal lenses, which correct for LCA by assigning concentric zones to correctly focus specific wavelengths. Each zone receives light from a specific beam entrance position (BEP) (the lateral distance between incoming light and the center of the lens). Any occlusion of incoming light at specific BEPs changes the composition of the wavelengths that are correctly focused on the retina. Here, we calculated the effect of lens position relative to the plane of the iris and light entering the eye at oblique angles on how much of the lens was involved in focusing the image on the retina (measured as the availability of BEPs). We used rotational photography of fish eyes and mathematical modeling to quantify the degree of lens occlusion. We found that, at most lens positions and viewing angles, there was a decrease of BEP availability and in some cases complete absence of some BEPs. Given the implications of these effects on image quality, we postulate that three morphological features (aphakic spaces, curvature of the iris, and intraretinal variability in spectral sensitivity) may, in part, be adaptations to mitigate the loss of spectral image quality in the periphery of the eyes of fishes.

Space experiment using large-sized fish: in case of carp in Spacelab-J mission.

PubMed

Mori, S; Mitarai, G; Takagi, S; Takabayashi, A; Usui, S; Nakamura, T; Sakakibara, M; Nagatomo, M; von Baumgarten, R J

1994-07-01

Two carp of 26 cm in size, intact and otolith-removed (LB), were flown on the Spacelab-J for 8 days in September 12-20, 1992. Light-dependent reaction to alternating direction of illumination was recorded for 10 min twice a day together with the cerebellar EEG activity, on 2 days before the launch, during the flight and for 4 days after the landing, in same fish chamber. Reproducing the video image, it was revealed that both carp were healthy during the mission, but the LB fish was almost immobilized from the 3rd test session (48 hours in flight) by tight twisting of the EEG cable. Both fish after landing tended to stay still on the bottom of the fish chamber. Findings that the body weight reduced remarkably in both fish and that nitrite and nitrate levels of the fish water were usually high, suggested that the fish metabolism might have been enhanced during the flight.

Over-the-counter fish oil use in a county hospital: Medication use evaluation and efficacy analysis

PubMed Central

Tatachar, Amulya; Pio, Margaret; Yeung, Denise; Moss, Elizabeth; Chow, Diem; Boatright, Steven; Quinones, Marissa; Mathew, Annie; Hulstein, Jeffrey; Adams-Huet, Beverley; Ahmad, Zahid

2016-01-01

BACKGROUND Little is known about the use and effectiveness of over-the-counter (OTC) fish oil supplements for triglyceride (TG) lowering. OBJECTIVES To (1) perform a medication-use evaluation (MUE) and (2) assess the efficacy of OTC fish oil. METHODS Retrospective, observational cohort study using electronic medical records and the pharmacy database from Parkland Health and Hospital System in Dallas, Texas. Parkland is a tax-supported county institution that provides patients with single-brand OTC fish oil. Two separate analyses were conducted. Six hundred seventeen patients (prescribed fish oil between July 1, 2012, and August 31, 2012) were included in the MUE analysis and 235 patients (109 fish oil, 72 fenofibrate, and 54 gemfibrozil, prescribed between January 1, 2012, and July 31, 2013) were included in the efficacy analysis. The main outcome measure for the MUE was fish oil prescribing habits including dosages and patient adherence, as defined by medication possession ratio. The main outcome measure for the efficacy analysis was change in lipids measured using the last value before fish oil treatment and the first value after fish oil treatment. RESULTS MUE: 617 patients received prescriptions for OTC fish oil. Sixty-four percent were prescribed a total daily dose of 2000 mg. Only 25% of patients were adherent. Efficacy analysis: despite being prescribed suboptimal doses, fish oil reduced TGs by 29% (95% confidence interval, 34.3–22.7). Compared with fish oil therapy, fibrate therapy resulted in a greater TG reduction: 48.5% (55.1–41.0) with fenofibrate and 49.8% (57.6–40.5) with gemfibrozil (P < 0001, both medications compared with fish oil). CONCLUSIONS Health care providers prescribe suboptimal doses of fish oil, and adherence is poor. Even at low doses (2 g/d), though, fish oil lowers TGs by 29%. PMID:26073390

Assessing the suitability of a remotely operated vehicle (ROV) to study the fish community associated with offshore gas platforms in the Ionian Sea: a comparative analysis with underwater visual censuses (UVCs)

NASA Astrophysics Data System (ADS)

Andaloro, Franco; Ferraro, Maria; Mostarda, Edoardo; Romeo, Teresa; Consoli, Pierpaolo

2013-06-01

The effectiveness of a remotely operated vehicle (ROV) to describe the fish communities of three gas platforms located offshore Crotone (Italy, Ionian Sea) was investigated by comparing its observations with underwater visual censuses (UVCs). The study was carried out at two depth layers (0-6 and 12-18 m). Moreover, the ROV was used to survey three deeper depth layers up to 76 m. Overall, the ROV surveys failed to give a truthful representation of the fish communities underestimating the number of species and their abundances as compared to UVCs. The main discrepancies in data regarded crypto-benthic and nekto-benthic species, whereas the ROV proved to be a suitable method to census low-mobile and abundant planktivorous species. The differences between the fish assemblage described by the ROV, with respect to the one depicted by UVC, should be considered in the light of the technical limits of the recording camera, whose resolution and field of vision is clearly lower than the diver's eye. In addition, video images did not allow for the acquisition of a correct estimate of the distance between the individuals and the platform structures. This led, almost certainly, to an under- or over-estimation of fish abundance as regards to the censused volume. In spite of this, as a result of its capacity to reach depths inaccessible to scuba divers and then to add complementary information, the ROV could be used jointly with UVCs, in studies having as their objective the description of the fish communities associated with offshore platforms.

Ocean in Motion

NASA Technical Reports Server (NTRS)

1999-01-01

Under a data purchase agreement with Goddard Space Flight Center, Orbital Sciences Corporation has been able to contract building of the Sea-Viewing Wide-Field-of-View Sensor (SeaWIFS). Orbital Sciences was then able commercialized the data that the satellite produces. These data are used to create daily fish finding maps, allowing fishing fleets to focus on locations where many commercially important surface feeding fish, like tuna and swordfish, congregate. In agriculture and forestry, SeaWIFS' images offer an alternative to direct on-site inspection or expensive serial photography.

Management and Feasibility Analysis of Smoked Fish Business in Ambon

NASA Astrophysics Data System (ADS)

Nanlohy, Hellen; Apituley, Yolanda M. T. N.; Tapotubun, Alfonsina M.; Reiuwpassa, Frederik; Matrutty, Theodora E. A. A.

2017-10-01

This research aims to examine management and feasibility aspects of smoked fish business in Ambon. By using survey, this research focused on smoked fish business in Negeri Hative Kecil and Silale, known as dried fish producer villages.Primary and secondary data collected by using interview, observation, and recording. Analysis methods used are qualitative descriptive analysis and business feasibility analysis covers NPV, Payback Period (PP), and Break Even Point (BEP). The result shows that most of the smoked fish businessmen do not apply the proper management in their business. Two to three people do all the works (from production to marketing) without a clear job description. Feasibility analysis for smoked fish business in Negeri Hative Kecil shows that NPV is 21.501.053,- PP is 58 days, and Benefit Cost Ratio (B/C) is 1,06. BEP Production is 1,455 kg, and BEP Price is IDR 19,941, while the feasibility analysis for smoked fish business in Desa Silale shows that NPV is 30.745.837,-, PP is 24 days and Benefit Cost Ratio (B/C) is 1,41. BEP Production is 988 kg, and BEP Price is IDR 7,966. Based on the result, the two smoked fish business in Ambon is feasible to be developed. However, good management with clear job description should be applied to improve the business.

Habitats as Surrogates of Taxonomic and Functional Fish Assemblages in Coral Reef Ecosystems: A Critical Analysis of Factors Driving Effectiveness

PubMed Central

Van Wynsberge, Simon; Andréfouët, Serge; Hamel, Mélanie A.; Kulbicki, Michel

2012-01-01

Species check-lists are helpful to establish Marine Protected Areas (MPAs) and protect local richness, endemicity, rarity, and biodiversity in general. However, such exhaustive taxonomic lists (i.e., true surrogate of biodiversity) require extensive and expensive censuses, and the use of estimator surrogates (e.g., habitats) is an appealing alternative. In truth, surrogate effectiveness appears from the literature highly variable both in marine and terrestrial ecosystems, making it difficult to provide practical recommendations for managers. Here, we evaluate how the biodiversity reference data set and its inherent bias can influence effectiveness. Specifically, we defined habitats by geomorphology, rugosity, and benthic cover and architecture criteria, and mapped them with satellite images for a New-Caledonian site. Fish taxonomic and functional lists were elaborated from Underwater Visual Censuses, stratified according to geomorphology and exposure. We then tested if MPA networks designed to maximize habitat richness, diversity and rarity could also effectively maximize fish richness, diversity, and rarity. Effectiveness appeared highly sensitive to the fish census design itself, in relation to the type of habitat map used and the scale of analysis. Spatial distribution of habitats (estimator surrogate’s distribution), quantity and location of fish census stations (target surrogate’s sampling), and random processes in the MPA design all affected effectiveness to the point that one small change in the data set could lead to opposite conclusions. We suggest that previous conclusions on surrogacy effectiveness, either positive or negative, marine or terrestrial, should be considered with caution, except in instances where very dense data sets were used without pseudo-replication. Although this does not rule out the validity of using surrogates of species lists for conservation planning, the critical joint examination of both target and estimator surrogates is needed for every case study. PMID:22815891

Analysis of habitat characteristics of small pelagic fish based on generalized additive models in Kepulauan Seribu Waters

NASA Astrophysics Data System (ADS)

Rivai, A. A.; Siregar, V. P.; Agus, S. B.; Yasuma, H.

2018-03-01

One of the required information for sustainable fisheries management is about the habitat characteristics of a fish species. This information can be used to map the distribution of fish and map the potential fishing ground. This study aimed to analyze the habitat characteristics of small pelagic fishes (anchovy, squid, sardine and scads) which were mainly caught by lift net in Kepulauan Seribu waters. Research on habitat characteristics had been widely done, but the use of total suspended solid (TSS) parameters in this analysis is still lacking. TSS parameter which was extracted from Landsat 8 along with five other oceanographic parameters, CPUE data and location of fishing ground data from lift net fisheries in Kepulauan Seribu were included in this analysis. This analysis used Generalized Additive Models (GAMs) to evaluate the relationship between CPUE and oceanographic parameters. The results of the analysis showed that each fish species had different habitat characteristics. TSS and sea surface height had a great influence on the value of CPUE from each species. All the oceanographic parameters affected the CPUE of each species. This study demonstrated the effective use of GAMs to identify the essential habitat of a fish species.

Identification of a duplication of Xq28 associated with bilateral periventricular nodular heterotopia.

PubMed Central

Fink, J M; Dobyns, W B; Guerrini, R; Hirsch, B A

1997-01-01

Bilateral periventricular nodular heterotopia (BPNH) is a malformation of neuronal migration and is characterized by nodules of heterotopic gray matter lining the lateral ventricles of the brain. The majority of BPNH patients are female and have epilepsy as a sole clinical manifestation of their disease. Familial BPNH has been mapped to Xq28 by linkage analysis. A multiple congenital anomaly-mental retardation syndrome (BPNH/MR) was recently delineated in three unrelated boys with BPNH, cerebellar hypoplasia, severe mental retardation, epilepsy, and syndactyly. High-resolution chromosome analysis revealed a subtle abnormality of Xq28 in one of the boys with BPNH/MR syndrome. FISH with cosmids and YACs from Xq28 further characterized this abnormality as a 2.25-3.25-Mb inverted duplication. No abnormality of Xq28 was detected by G-banding or FISH in the other two boys. These data support the linkage assignment of BPNH to band Xq28 and narrow the critical region to the distal 2.25-3.25 Mb of Xq28. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:9311743

Use of baited remote underwater video (BRUV) and motion analysis for studying the impacts of underwater noise upon free ranging fish and implications for marine energy management.

PubMed

Roberts, Louise; Pérez-Domínguez, Rafael; Elliott, Michael

2016-11-15

Free-ranging individual fish were observed using a baited remote underwater video (BRUV) system during sound playback experiments. This paper reports on test trials exploring BRUV design parameters, image analysis and practical experimental designs. Three marine species were exposed to playback noise, provided as examples of behavioural responses to impulsive sound at 163-171dB re 1μPa (peak-to-peak SPL) and continuous sound of 142.7dB re 1μPa (RMS, SPL), exhibiting directional changes and accelerations. The methods described here indicate the efficacy of BRUV to examine behaviour of free-ranging species to noise playback, rather than using confinement. Given the increasing concern about the effects of water-borne noise, for example its inclusion within the EU Marine Strategy Framework Directive, and the lack of empirical evidence in setting thresholds, this paper discusses the use of BRUV, and short term behavioural changes, in supporting population level marine noise management. Copyright © 2016 Elsevier Ltd. All rights reserved.

USE OF MULTIPHOTON LASER SCANNING MICROSCOPY TO IMAGE BENZO[A]PYRENE AND METABOLITES IN FISH EARLY LIFE STAGES

EPA Science Inventory

Multiphoton laser scanning micrsocopy holds promise as a tool to study the tissue distribution of environmental chemical contaminants during fish early life stage development. One such chemical for which this is possible is benzo[a]pyrene (BaP), a polyaromatic hydrocarbon that a...

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

PubMed

Mader, Malte; Simon, Ronald; Kurtz, Stefan

2014-03-31

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.

SAR-based sea traffic monitoring: a reliable approach for maritime surveillance

NASA Astrophysics Data System (ADS)

Renga, Alfredo; Graziano, Maria D.; D'Errico, M.; Moccia, A.; Cecchini, A.

2011-11-01

Maritime surveillance problems are drawing the attention of multiple institutional actors. National and international security agencies are interested in matters like maritime traffic security, maritime pollution control, monitoring migration flows and detection of illegal fishing activities. Satellite imaging is a good way to identify ships but, characterized by large swaths, it is likely that the imaged scenes contain a large number of ships, with the vast majority, hopefully, performing legal activities. Therefore, the imaging system needs a supporting system which identifies legal ships and limits the number of potential alarms to be further monitored by patrol boats or aircrafts. In this framework, spaceborne Synthetic Aperture Radar (SAR) sensors, terrestrial AIS and the ongoing satellite AIS systems can represent a great potential synergy for maritime security. Starting from this idea the paper develops different designs for an AIS constellation able to reduce the time lag between SAR image and AIS data acquisition. An analysis of SAR-based ship detection algorithms is also reported and candidate algorithms identified.

Partial sequencing of sodA gene and its application to identification of Streptococcus dysgalactiae subsp. dysgalactiae isolated from farmed fish.

PubMed

Nomoto, R; Kagawa, H; Yoshida, T

2008-01-01

To investigate the difference between Lancefield group C Streptococcus dysgalactiae (GCSD) strains isolated from diseased fish and animals by sequencing and phylogenetic analysis of the sodA gene. The sodA gene of Strep. dysgalactiae strains isolated from fish and animals were amplified and its nucleotide sequences were determined. Although 100% sequence identity was observed among fish GCSD strains, the determined sequences from animal isolates showed variations against fish isolate sequences. Thus, all fish GCSD strains were clearly separated from the GCSD strains of other origin by using phylogenetic tree analysis. In addition, the original primer set was designed based on the determined sequences for specifically amplify the sodA gene of fish GCSD strains. The primer set yield amplification products from only fish GCSD strains. By sequencing analysis of the sodA gene, the genetic divergence between Strep. dysgalactiae strains isolated from fish and mammals was demonstrated. Moreover, an original oligonucletide primer set, which could simply detect the genotype of fish GCSD strains was designed. This study shows that Strep. dysgalactiae isolated from diseased fish could be distinguished from conventional GCSD strains by the difference in the sequence of the sodA gene.

Fish and Robots Swimming Together in a Water Tunnel: Robot Color and Tail-Beat Frequency Influence Fish Behavior

PubMed Central

Polverino, Giovanni; Phamduy, Paul; Porfiri, Maurizio

2013-01-01

The possibility of integrating bioinspired robots in groups of live social animals may constitute a valuable tool to study the basis of social behavior and uncover the fundamental determinants of animal functions and dysfunctions. In this study, we investigate the interactions between individual golden shiners (Notemigonus crysoleucas) and robotic fish swimming together in a water tunnel at constant flow velocity. The robotic fish is designed to mimic its live counterpart in the aspect ratio, body shape, dimension, and locomotory pattern. Fish positional preference with respect to the robot is experimentally analyzed as the robot's color pattern and tail-beat frequency are varied. Behavioral observations are corroborated by particle image velocimetry studies aimed at investigating the flow structure behind the robotic fish. Experimental results show that the time spent by golden shiners in the vicinity of the bioinspired robotic fish is the highest when the robot mimics their natural color pattern and beats its tail at the same frequency. In these conditions, fish tend to swim at the same depth of the robotic fish, where the wake from the robotic fish is stronger and hydrodynamic return is most likely to be effective. PMID:24204882

Fish and robots swimming together in a water tunnel: robot color and tail-beat frequency influence fish behavior.

PubMed

Polverino, Giovanni; Phamduy, Paul; Porfiri, Maurizio

2013-01-01

The possibility of integrating bioinspired robots in groups of live social animals may constitute a valuable tool to study the basis of social behavior and uncover the fundamental determinants of animal functions and dysfunctions. In this study, we investigate the interactions between individual golden shiners (Notemigonus crysoleucas) and robotic fish swimming together in a water tunnel at constant flow velocity. The robotic fish is designed to mimic its live counterpart in the aspect ratio, body shape, dimension, and locomotory pattern. Fish positional preference with respect to the robot is experimentally analyzed as the robot's color pattern and tail-beat frequency are varied. Behavioral observations are corroborated by particle image velocimetry studies aimed at investigating the flow structure behind the robotic fish. Experimental results show that the time spent by golden shiners in the vicinity of the bioinspired robotic fish is the highest when the robot mimics their natural color pattern and beats its tail at the same frequency. In these conditions, fish tend to swim at the same depth of the robotic fish, where the wake from the robotic fish is stronger and hydrodynamic return is most likely to be effective.

Development of low level 226Ra analysis for live fish using gamma-ray spectrometry

NASA Astrophysics Data System (ADS)

Chandani, Z.; Prestwich, W. V.; Byun, S. H.

2017-06-01

A low level 226Ra analysis method for live fish was developed using a 4π NaI(Tl) gamma-ray spectrometer. In order to find out the best algorithm for accomplishing the lowest detection limit, the gamma-ray spectrum from a 226Ra point was collected and nine different methods were attempted for spectral analysis. The lowest detection limit of 0.99 Bq for an hour counting occurred when the spectrum was integrated in the energy region of 50-2520 keV. To extend 226Ra analysis to live fish, a Monte Carlo simulation model with a cylindrical fish in a water container was built using the MCNP code. From simulation results, the spatial distribution of the efficiency and the efficiency correction factor for the live fish model were determined. The MCNP model will be able to be conveniently modified when a different fish or container geometry is employed as fish grow up in real experiments.

Hagfish predatory behaviour and slime defence mechanism

PubMed Central

Zintzen, Vincent; Roberts, Clive D.; Anderson, Marti J.; Stewart, Andrew L.; Struthers, Carl D.; Harvey, Euan S.

2011-01-01

Hagfishes (Myxinidae), a family of jawless marine pre-vertebrates, hold a unique evolutionary position, sharing a joint ancestor with the entire vertebrate lineage. They are thought to fulfil primarily the ecological niche of scavengers in the deep ocean. However, we present new footage from baited video cameras that captured images of hagfishes actively preying on other fish. Video images also revealed that hagfishes are able to choke their would-be predators with gill-clogging slime. This is the first time that predatory behaviour has been witnessed in this family, and also demonstrates the instantaneous effectiveness of hagfish slime to deter fish predators. These observations suggest that the functional adaptations and ecological role of hagfishes, past and present, might be far more diverse than previously assumed. We propose that the enduring success of this oldest extant family of fishes over 300 million years could largely be due to their unique combination of functional traits. PMID:22355648

Imaging Techniques for Dense 3D reconstruction of Swimming Aquatic Life using Multi-view Stereo

NASA Astrophysics Data System (ADS)

Daily, David; Kiser, Jillian; McQueen, Sarah

2016-11-01

Understanding the movement characteristics of how various species of fish swim is an important step to uncovering how they propel themselves through the water. Previous methods have focused on profile capture methods or sparse 3D manual feature point tracking. This research uses an array of 30 cameras to automatically track hundreds of points on a fish as they swim in 3D using multi-view stereo. Blacktip sharks, sting rays, puffer fish, turtles and more were imaged in collaboration with the National Aquarium in Baltimore, Maryland using the multi-view stereo technique. The processes for data collection, camera synchronization, feature point extraction, 3D reconstruction, 3D alignment, biological considerations, and lessons learned will be presented. Preliminary results of the 3D reconstructions will be shown and future research into mathematically characterizing various bio-locomotive maneuvers will be discussed.

Facial Recognition in a Group-Living Cichlid Fish.

PubMed

Kohda, Masanori; Jordan, Lyndon Alexander; Hotta, Takashi; Kosaka, Naoya; Karino, Kenji; Tanaka, Hirokazu; Taniyama, Masami; Takeyama, Tomohiro

2015-01-01

The theoretical underpinnings of the mechanisms of sociality, e.g. territoriality, hierarchy, and reciprocity, are based on assumptions of individual recognition. While behavioural evidence suggests individual recognition is widespread, the cues that animals use to recognise individuals are established in only a handful of systems. Here, we use digital models to demonstrate that facial features are the visual cue used for individual recognition in the social fish Neolamprologus pulcher. Focal fish were exposed to digital images showing four different combinations of familiar and unfamiliar face and body colorations. Focal fish attended to digital models with unfamiliar faces longer and from a further distance to the model than to models with familiar faces. These results strongly suggest that fish can distinguish individuals accurately using facial colour patterns. Our observations also suggest that fish are able to rapidly (≤ 0.5 sec) discriminate between familiar and unfamiliar individuals, a speed of recognition comparable to primates including humans.

Relative impacts of the fragmentation and spatial structure of habitats on freshwater fish distributions: application on French watersheds (Invited)

NASA Astrophysics Data System (ADS)

Le Pichon, C.; Belliard, J.; Talès, E.; Gorges, G.; Clément, F.

2009-12-01

Most of the rivers of the Ile de France region, intimately linked with the megalopolis of Paris, are severely altered and freshwater fishes are exposed to habitat alteration, reduced connectivity and pollution. Several species thus present fragmented distributions and decreasing densities. In this context, the European Water Framework Directive (2000) has goals of hydrosystems rehabilitation and no further damage. In particular, the preservation and restoration of ecological connectivity of river networks is a key element for fish populations. These goals require the identification of natural and anthropological factors which influence the spatial distribution of species. We have proposed a riverscape approach, based on landscape ecology concepts, combined with a set of spatial analysis methods to assess the multiscale relationships between the spatial pattern of fish habitats and processes depending on fish movements. In particular, we used this approach to test the relative roles of spatial arrangement of fish habitats and the presence of physical barriers in explaining fish spatial distributions in a small rural watershed (106 km2). We performed a spatially continuous analysis of fish-habitat relationships. Fish habitats and physical barriers were mapped along the river network (33 km) with a GPS and imported into a GIS. In parallel, a longitudinal electrofishing survey of the distribution and abundance of fishes was made using a point abundance sampling scheme. Longitudinal arrangement of fish habitats were evaluated using spatial analysis methods: patch/distance metrics and moving window analysis. Explanatory models were developed to test the relative contribution of local environmental variables and spatial context in explaining fish presence. We have recorded about 100 physical barriers, on average one every 330 meters; most artificial barriers were road pipe culverts, falls associated with ponds and sluice gates. Contrasted fish communities and densities were observed in the different areas of the watershed, related to various land use (riparian forest or agriculture). The first results of fish-habitat association analysis on a 5 km stream are that longitudinal distribution of fish species was mainly impacted by falls associated with ponds. The impact was both due to the barrier effect and to the modification of aquatic habitats. Abundance distribution of Salmo trutta and Cottus gobio was particularly affected. Spatially continuous analysis of fish-habitat relationships allowed us to identify the relative impacts of habitat alteration and presence of physical barriers to fish movements. These techniques could help prioritize preservation and restoration policies in human-impacted watersheds, in particular, identifying the key physical barriers to remove.

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells.

PubMed

Guedes, Ana M V; Henrique, Domingos; Abranches, Elsa

2016-01-01

Mouse Embryonic Stem cells (mESCs) show heterogeneous and dynamic expression of important pluripotency regulatory factors. Single-cell analysis has revealed the existence of cell-to-cell variability in the expression of individual genes in mESCs. Understanding how these heterogeneities are regulated and what their functional consequences are is crucial to obtain a more comprehensive view of the pluripotent state.In this chapter we describe how to analyze transcriptional heterogeneity by monitoring gene expression of Nanog, Oct4, and Sox2, using single-molecule RNA FISH in single mESCs grown in different cell culture medium. We describe in detail all the steps involved in the protocol, from RNA detection to image acquisition and processing, as well as exploratory data analysis.

Sound extinction by fish schools: forward scattering theory and data analysis.

PubMed

Raveau, M; Feuillade, C

2015-02-01

A model used previously to study collective back scattering from fish schools [Feuillade et al., J. Acoust. Soc. Am. 99(1), 196-208 (1996)], is used to analyze the forward scattering properties of these objects. There is an essential physical difference between back and forward scattering from fish schools. Strong frequency dependent interference effects, which affect the back scattered field amplitude, are absent in the forward scattering case. This is critically important for data analysis. There is interest in using back scattering and transmission data from fish schools to study their size, the species and abundance of fish, and fish behavior. Transmission data can be processed to determine the extinction of the field by a school. The extinction of sound depends on the forward scattering characteristics of the school, and data inversion to provide information about the fish should be based upon a forward scattering paradigm. Results are presented of an analysis of transmission data obtained in September 1995 during an experiment performed in the Gulf of Lion in the Mediterranean Sea [Diachok, J. Acoust. Soc. Am. 105(4), 2107-2128 (1999)]. The analysis shows that using forward scattering leads to significantly larger estimates of fish abundance than previous analysis based upon back scattering approaches.

Screening for specific chromosome involvement in hematological malignancies using a set of seven chromosome painting probes. An alternative approach for chromosome analysis using standard FISH instrumentation.

PubMed

Nacheva, E P; Gribble, S; Andrews, K; Wienberg, J; Grace, C D

2000-10-15

We report the application of multi-color fluorescence in situ hydribidization (FISH) for bone marrow metaphase cell analysis of hematological malignancies using a sub-set of the human karyotype for chromosome painting. A combination of chromosome probes labeled with three haptens enabled the construction of a "painting probe" which detects seven different chromosomes. The probe was used to screen three chronic myeloid leukemia (CML) derived cell lines and ten CML patient bone marrow samples for aberrations, additional to the Ph rearrangement, that are associated with the onset of blast crisis of CML. This approach was shown to identify karyotype changes commonly seen by conventional karyotyping, and in addition revealed chromosome changes unresolved or undetected by conventional cytogenetic analysis. The seven-color painting probe provides a useful, fast, and reliable complementary tool for chromosome analysis, especially in cases with poor chromosome morphology. This is a simple approach, since the probes can be displayed in a standard red/green/blue format accessible to standard fluorescence microscopes and image-processing software. The proposed approach using panels of locus-specific probes as well as chromosome paints will be useful in all diagnostic routine environments where analysis is directed towards screening for genetic rearrangements and/or specific patterns of chromosome involvement with diagnostic/prognostic value.

Comparison of fish and macroinvertebrates as bioindicators of Neotropical streams.

PubMed

Ruaro, Renata; Gubiani, Éder André; Cunico, Almir Manoel; Moretto, Yara; Piana, Pitágoras Augusto

2016-01-01

The biomonitoring of aquatic ecosystems in developing countries faces several limitations, especially related to gathering resources. The present study aimed at comparing the responses of fish and benthic macroinvertebrates to environmental change, to identify which group best indicates the differences between reference and impacted streams in southern Brazil. We determined reference and impacted sites based on physical and chemical variables of the water. For the analysis and comparison of biological responses, we calculated 22 metrics and submitted them to a discriminant analysis. We selected from this analysis only six metrics, which showed that the two studied assemblages respond differently to environmental change. A larger number of metrics were selected for macroinvertebrates than for fish in the separate analysis. The metrics selected for macroinvertebrates in the pooled analysis (i.e., fish and macroinvertebrates together) were different from those selected in the separate analysis for macroinvertebrates alone. However, the metrics selected for fish in the pooled analysis were the same selected in the separate analysis for fish alone. The macroinvertebrate assemblage was more effective for distinguishing reference from impacted sites. We suggest the use of macroinvertebrates as bioindicators of Neotropical streams, especially in situations in which time and money are short.

Automated biodosimetry using digital image analysis of fluorescence in situ hybridization specimens.

PubMed

Castleman, K R; Schulze, M; Wu, Q

1997-11-01

Fluorescence in situ hybridization (FISH) of metaphase chromosome spreads is valuable for monitoring the radiation dose to circulating lymphocytes. At low dose levels, the number of cells that must be examined to estimate aberration frequencies is quite large. An automated microscope that can perform this analysis autonomously on suitably prepared specimens promises to make practical the large-scale studies that will be required for biodosimetry in the future. This paper describes such an instrument that is currently under development. We use metaphase specimens in which the five largest chromosomes have been hybridized with different-colored whole-chromosome painting probes. An automated multiband fluorescence microscope locates the spreads and counts the number of chromosome components of each color. Digital image analysis is used to locate and isolate the cells, count chromosome components, and estimate the proportions of abnormal cells. Cells exhibiting more than two chromosomal fragments in any color correspond to a clastogenic event. These automatically derived counts are corrected for statistical bias and used to estimate the overall rate of chromosome breakage. Overlap of fluorophore emission spectra prohibits isolation of the different chromosomes into separate color channels. Image processing effectively isolates each fluorophore to a single monochrome image, simplifying the task of counting chromosome fragments and reducing the error in the algorithm. Using proportion estimation, we remove the bias introduced by counting errors, leaving accuracy restricted by sample size considerations alone.

Preparation of Microkernel-Based Mesoporous (SiO2-CdTe-SiO2)@SiO2 Fluorescent Nanoparticles for Imaging Screening and Enrichment of Heat Shock Protein 90 Inhibitors from Tripterygium Wilfordii.

PubMed

Hu, Yue; Miao, Zhao-Yi; Zhang, Xiao-Jing; Yang, Xiao-Tong; Tang, Ying-Ying; Yu, Sheng; Shan, Chen-Xiao; Wen, Hong-Mei; Zhu, Dong

2018-05-01

The currently utilized ligand fishing for bioactive molecular screening from complex matrixes cannot perform imaging screening. Here, we developed a new solid-phase ligand fishing coupled with an in situ imaging protocol for the specific enrichment and identification of heat shock protein 90 (Hsp 90) inhibitors from Tripterygium wilfordii, utilizing a multiple-layer and microkernel-based mesoporous nanostructure composed of a protective silica coating CdTe quantum dot (QD) core and a mesoporous silica shell, i.e., microkernel-based mesoporous (SiO 2 -CdTe-SiO 2 )@SiO 2 fluorescent nanoparticles (MMFNPs) as extracting carries and fluorescent probes. The prepared MMFNPs showed a highly uniform spherical morphology, retention of fluorescence emission, and great chemical stability. The fished ligands by Hsp 90α-MMFNPs were evaluated via the preliminary bioactivity based on real-time cellular morphology imaging by confocal laser scanning microscopy (CLSM) and then identified by mass spectrometry (MS). Celastrol was successfully isolated as an Hsp 90 inhibitor, and two other specific components screened by Hsp 90α-MMFNPs, i.e., demecolcine and wilforine, were preliminarily identified as potential Hsp 90 inhibitors through the verification of strong affinity to Hsp 90 and antitumor bioactivity. The approach based on the MMFNPs provides a strong platform for imaging screening and discovery of plant-derived biologically active molecules with high efficiency and selectivity.

Fish assemblages

USGS Publications Warehouse

McGarvey, Daniel J.; Falke, Jeffrey A.; Li, Hiram W.; Li, Judith; Hauer, F. Richard; Lamberti, G.A.

2017-01-01

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

Fish Geometry and Electric Organ Discharge Determine Functional Organization of the Electrosensory Epithelium

PubMed Central

Sanguinetti-Scheck, Juan Ignacio; Pedraja, Eduardo Federico; Cilleruelo, Esteban; Migliaro, Adriana; Aguilera, Pedro; Caputi, Angel Ariel; Budelli, Ruben

2011-01-01

Active electroreception in Gymnotus omarorum is a sensory modality that perceives the changes that nearby objects cause in a self generated electric field. The field is emitted as repetitive stereotyped pulses that stimulate skin electroreceptors. Differently from mormyriformes electric fish, gymnotiformes have an electric organ distributed along a large portion of the body, which fires sequentially. As a consequence shape and amplitude of both, the electric field generated and the image of objects, change during the electric pulse. To study how G. omarorum constructs a perceptual representation, we developed a computational model that allows the determination of the self-generated field and the electric image. We verify and use the model as a tool to explore image formation in diverse experimental circumstances. We show how the electric images of objects change in shape as a function of time and position, relative to the fish's body. We propose a theoretical framework about the organization of the different perceptive tasks made by electroreception: 1) At the head region, where the electrosensory mosaic presents an electric fovea, the field polarizing nearby objects is coherent and collimated. This favors the high resolution sampling of images of small objects and perception of electric color. Besides, the high sensitivity of the fovea allows the detection and tracking of large faraway objects in rostral regions. 2) In the trunk and tail region a multiplicity of sources illuminate different regions of the object, allowing the characterization of the shape and position of a large object. In this region, electroreceptors are of a unique type and capacitive detection should be based in the pattern of the afferents response. 3) Far from the fish, active electroreception is not possible but the collimated field is suitable to be used for electrocommunication and detection of large objects at the sides and caudally. PMID:22096578

Fish oil supplementation and insulin sensitivity: a systematic review and meta-analysis.

PubMed

Gao, Huanqing; Geng, Tingting; Huang, Tao; Zhao, Qinghua

2017-07-03

Fish oil supplementation has been shown to be associated with a lower risk of metabolic syndrome and benefit a wide range of chronic diseases, such as cardiovascular disease, type 2 diabetes and several types of cancers. However, the evidence of fish oil supplementation on glucose metabolism and insulin sensitivity is still controversial. This meta-analysis summarized the exist evidence of the relationship between fish oil supplementation and insulin sensitivity and aimed to evaluate whether fish oil supplementation could improve insulin sensitivity. We searched the Cochrane Library, PubMed, Embase database for the relevant studies update to Dec 2016. Two researchers screened the literature independently by the selection and exclusion criteria. Studies were pooled using random effect models to estimate a pooled SMD and corresponding 95% CI. This meta-analysis was performed by Stata 13.1 software. A total of 17 studies with 672 participants were included in this meta-analysis study after screening from 498 published articles found after the initial search. In a pooled analysis, fish oil supplementation had no effects on insulin sensitivity compared with the placebo (SMD 0.17, 95%CI -0.15 to 0.48, p = 0.292). In subgroup analysis, fish oil supplementation could benefit insulin sensitivity among people who were experiencing at least one symptom of metabolic disorders (SMD 0.53, 95% CI 0.17 to 0.88, p < 0.001). Similarly, there were no significant differences between subgroups of methods of insulin sensitivity, doses of omega-3 polyunsaturated fatty acids (n-3 PUFA) of fish oil supplementation or duration of the intervention. The sensitivity analysis indicated that the results were robust. Short-term fish oil supplementation is associated with increasing the insulin sensitivity among those people with metabolic disorders.

Accelerated Optical Projection Tomography Applied to In Vivo Imaging of Zebrafish

PubMed Central

Correia, Teresa; Yin, Jun; Ramel, Marie-Christine; Andrews, Natalie; Katan, Matilda; Bugeon, Laurence; Dallman, Margaret J.; McGinty, James; Frankel, Paul; French, Paul M. W.; Arridge, Simon

2015-01-01

Optical projection tomography (OPT) provides a non-invasive 3-D imaging modality that can be applied to longitudinal studies of live disease models, including in zebrafish. Current limitations include the requirement of a minimum number of angular projections for reconstruction of reasonable OPT images using filtered back projection (FBP), which is typically several hundred, leading to acquisition times of several minutes. It is highly desirable to decrease the number of required angular projections to decrease both the total acquisition time and the light dose to the sample. This is particularly important to enable longitudinal studies, which involve measurements of the same fish at different time points. In this work, we demonstrate that the use of an iterative algorithm to reconstruct sparsely sampled OPT data sets can provide useful 3-D images with 50 or fewer projections, thereby significantly decreasing the minimum acquisition time and light dose while maintaining image quality. A transgenic zebrafish embryo with fluorescent labelling of the vasculature was imaged to acquire densely sampled (800 projections) and under-sampled data sets of transmitted and fluorescence projection images. The under-sampled OPT data sets were reconstructed using an iterative total variation-based image reconstruction algorithm and compared against FBP reconstructions of the densely sampled data sets. To illustrate the potential for quantitative analysis following rapid OPT data acquisition, a Hessian-based method was applied to automatically segment the reconstructed images to select the vasculature network. Results showed that 3-D images of the zebrafish embryo and its vasculature of sufficient visual quality for quantitative analysis can be reconstructed using the iterative algorithm from only 32 projections—achieving up to 28 times improvement in imaging speed and leading to total acquisition times of a few seconds. PMID:26308086

The star fish twins: Two young planetary nebulae with extreme multipolar morphology

NASA Technical Reports Server (NTRS)

Sahai, R.

2000-01-01

We present alpha images of two objects, He 2-47 and M1-37, obtained during a Hubble Space Telescope imaging survey of young planetary nebulae (PNs) selected on the basis of their low-excitation characteristics.

Genomic profiling of plasma cell disorders in a clinical setting: integration of microarray and FISH, after CD138 selection of bone marrow

PubMed Central

Berry, Nadine Kaye; Bain, Nicole L; Enjeti, Anoop K; Rowlings, Philip

2014-01-01

Aim To evaluate the role of whole genome comparative genomic hybridisation microarray (array-CGH) in detecting genomic imbalances as compared to conventional karyotype (GTG-analysis) or myeloma specific fluorescence in situ hybridisation (FISH) panel in a diagnostic setting for plasma cell dyscrasia (PCD). Methods A myeloma-specific interphase FISH (i-FISH) panel was carried out on CD138 PC-enriched bone marrow (BM) from 20 patients having BM biopsies for evaluation of PCD. Whole genome array-CGH was performed on reference (control) and neoplastic (test patient) genomic DNA extracted from CD138 PC-enriched BM and analysed. Results Comparison of techniques demonstrated a much higher detection rate of genomic imbalances using array-CGH. Genomic imbalances were detected in 1, 19 and 20 patients using GTG-analysis, i-FISH and array-CGH, respectively. Genomic rearrangements were detected in one patient using GTG-analysis and seven patients using i-FISH, while none were detected using array-CGH. I-FISH was the most sensitive method for detecting gene rearrangements and GTG-analysis was the least sensitive method overall. All copy number aberrations observed in GTG-analysis were detected using array-CGH and i-FISH. Conclusions We show that array-CGH performed on CD138-enriched PCs significantly improves the detection of clinically relevant and possibly novel genomic abnormalities in PCD, and thus could be considered as a standard diagnostic technique in combination with IGH rearrangement i-FISH. PMID:23969274

Genomic profiling of plasma cell disorders in a clinical setting: integration of microarray and FISH, after CD138 selection of bone marrow.

PubMed

Berry, Nadine Kaye; Bain, Nicole L; Enjeti, Anoop K; Rowlings, Philip

2014-01-01

To evaluate the role of whole genome comparative genomic hybridisation microarray (array-CGH) in detecting genomic imbalances as compared to conventional karyotype (GTG-analysis) or myeloma specific fluorescence in situ hybridisation (FISH) panel in a diagnostic setting for plasma cell dyscrasia (PCD). A myeloma-specific interphase FISH (i-FISH) panel was carried out on CD138 PC-enriched bone marrow (BM) from 20 patients having BM biopsies for evaluation of PCD. Whole genome array-CGH was performed on reference (control) and neoplastic (test patient) genomic DNA extracted from CD138 PC-enriched BM and analysed. Comparison of techniques demonstrated a much higher detection rate of genomic imbalances using array-CGH. Genomic imbalances were detected in 1, 19 and 20 patients using GTG-analysis, i-FISH and array-CGH, respectively. Genomic rearrangements were detected in one patient using GTG-analysis and seven patients using i-FISH, while none were detected using array-CGH. I-FISH was the most sensitive method for detecting gene rearrangements and GTG-analysis was the least sensitive method overall. All copy number aberrations observed in GTG-analysis were detected using array-CGH and i-FISH. We show that array-CGH performed on CD138-enriched PCs significantly improves the detection of clinically relevant and possibly novel genomic abnormalities in PCD, and thus could be considered as a standard diagnostic technique in combination with IGH rearrangement i-FISH.

"Good looks don’t boil the pot": Irish-Newfoundland women as fish(-producing) wives.

PubMed

Keough, Willeen

2012-01-01

This article explores the historical understanding of maritime womanhood in Newfoundland by examining women in fishing families along the southern Avalon Peninsula from the late eighteenth to the early twentieth centuries. It does not talk about fishwives in any popular sense of the word, for these women did not market fish; rather, they produced salt fish for market. And while middle-class observers may have perceived them as coarse and bold, within their own families and fishing communities they were seen as essential partners who contributed equally to family economies. Within a sexual division of labor that assigned vital and complementary tasks to both men and women, Newfoundland fish(-producing) wives carried out hard physical labor at public sites of production. This contributed significantly to the construction of “woman” as essential worker, which in turn had broader repercussions for their status and authority within fishing communities. The participation of fish(-producing) wives changed significantly from the 1950s onward, as the fishery moved from household production to a modernized, and discursively masculinized, industry. Yet the iconic image of the fish(-producing) wife in traditional household production remains undisrupted in the early twenty-first century.

Super resolution imaging of HER2 gene amplification

NASA Astrophysics Data System (ADS)

Okada, Masaya; Kubo, Takuya; Masumoto, Kanako; Iwanaga, Shigeki

2016-02-01

HER2 positive breast cancer is currently examined by counting HER2 genes using fluorescence in situ hybridization (FISH)-stained breast carcinoma samples. In this research, two-dimensional super resolution fluorescence microscopy based on stochastic optical reconstruction microscopy (STORM), with a spatial resolution of approximately 20 nm in the lateral direction, was used to more precisely distinguish and count HER2 genes in a FISH-stained tissue section. Furthermore, by introducing double-helix point spread function (DH-PSF), an optical phase modulation technique, to super resolution microscopy, three-dimensional images were obtained of HER2 in a breast carcinoma sample approximately 4 μm thick.

A Simplified Digestion Protocol for the Analysis of Hg in Fish by Cold Vapor Atomic Absorption Spectroscopy

ERIC Educational Resources Information Center

Kristian, Kathleen E.; Friedbauer, Scott; Kabashi, Donika; Ferencz, Kristen M.; Barajas, Jennifer C.; O'Brien, Kelly

2015-01-01

Analysis of mercury in fish is an interesting problem with the potential to motivate students in chemistry laboratory courses. The recommended method for mercury analysis in fish is cold vapor atomic absorption spectroscopy (CVAAS), which requires homogeneous analyte solutions, typically prepared by acid digestion. Previously published digestion…

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

PubMed Central

2014-01-01

Background A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. Results We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. Conclusions The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle. PMID:24684958

Automated Meteor Detection by All-Sky Digital Camera Systems

NASA Astrophysics Data System (ADS)

Suk, Tomáš; Šimberová, Stanislava

2017-12-01

We have developed a set of methods to detect meteor light traces captured by all-sky CCD cameras. Operating at small automatic observatories (stations), these cameras create a network spread over a large territory. Image data coming from these stations are merged in one central node. Since a vast amount of data is collected by the stations in a single night, robotic storage and analysis are essential to processing. The proposed methodology is adapted to data from a network of automatic stations equipped with digital fish-eye cameras and includes data capturing, preparation, pre-processing, analysis, and finally recognition of objects in time sequences. In our experiments we utilized real observed data from two stations.

The effect of fish meal replacement by soyabean products on fish growth: a meta-analysis.

PubMed

Sales, James

2009-12-01

Meta-analysis was applied to quantify the effect of replacement of fish meal by soyabean products in diets on fish growth. Measurement of growth in different units among studies required the use of a standardised effect size (Hedges' d). From a total of ninety-nine studies concentrating on fish meal replacement by defatted soyabean meal, 53 % were eliminated due to, among others, absence of a fish meal control diet (n 18), or no statistical differences or measurement of dispersion (n 6) indicated. Replacement of 4 to 40 % fish meal by soyabean meal (inclusion levels of 71-366 g/kg) resulted in a mean effect size of - 0.1142 (95 % CI - 0.4665, 0.2382) obtained in forty-eight comparisons evaluated with seventeen different fish species. However, at higher fish meal replacement levels the 95 % CI calculated for combined effect sizes did not overlap with zero. With soya protein concentrate replacing 25 to 100 % of fish meal in diets for seven fish species, methionine supplementation (mean - 2.4373 (95 % CI - 3.9004, - 0.9742); n 10) did not have a substantial influence on the magnitude of cumulative effect sizes relative to no supplementation (mean - 2.7306 (95 % CI - 3.7991, - 1.6620); n 16). Information on other soyabean products (full-fat soyabeans, soya flour) used as protein sources in fish diets was found as too limited for analysis and definite conclusions. The present study contributes by putting a numerical value to the magnitude of growth differences in fish when replacing dietary fish meal by soyabean products.

Cavisoma magnum (Cavisomidae), a unique Pacific acanthocephalan redescribed from an unusual host, Mugil cephalus (Mugilidae), in the Arabian Gulf, with notes on histopathology and metal analysis

PubMed Central

Amin, Omar M.; Heckmann, Richard A.; Bannai, Majid A.

2018-01-01

Cavisoma magnum (Southwell, 1927) Van Cleave, 1931 was originally described from a sea bass, Serranus sp. and spotted surgeonfish, Ctenochaetus strigosus (Perciformes) off Sri Lanka before its more recent redescription from milkfish in the Philippines in 1995. These reports were based on only light infections of their host fishes. Of the few flathead grey mullets, Mugil cephalus (Mugilidae), that we examined in the Arabian Gulf, one fish was infected with 1,450 worms. One milkfish, Chanos chanos (Chanidae), from the same location in the Arabian Gulf, was also heavily infected with specimens of C. magnum. The descriptions of this unique large worm are revised and for the first time, we provide SEM images, new systematic observations, metal analysis of hooks showing extremely high levels of sulfur, and histopathology in the mullet intestinal tissue. Adjustments and corrections of previous descriptive accounts are made. The histopathology studies show extensive damage to the host intestinal tissue including epithelial necrosis, hemorrhaging and worm encapsulation. There is an extensive amount of host connective tissue surrounding the worm. Results of x-ray analysis displayed high levels of sulfur in proboscis hooks, especially at the tips and edges of these attachment structures. PMID:29424340

Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments.

PubMed

Yuan, Zihao; Liu, Shikai; Zhou, Tao; Tian, Changxu; Bao, Lisui; Dunham, Rex; Liu, Zhanjiang

2018-02-13

Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.

Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis.

PubMed

Gorman, Bryan R; Lu, Junjie; Baccei, Anna; Lowry, Nathan C; Purvis, Jeremy E; Mangoubi, Rami S; Lerou, Paul H

2014-01-01

Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.

Antibody reactivity to the major fish allergen parvalbumin is determined by isoforms and impact of thermal processing.

PubMed

Saptarshi, Shruti R; Sharp, Michael F; Kamath, Sandip D; Lopata, Andreas L

2014-04-01

The EF-hand calcium binding protein, parvalbumin, is a major fish allergen. Detection of this allergen is often difficult due to its structural diversity among various fish species. The aim of this study was to evaluate the cross-reactivity of parvalbumin in a comprehensive range of bony and cartilaginous fish, from the Asia-Pacific region, and conduct a molecular analysis of this highly allergenic protein. Using the monoclonal anti-parvalbumin antibody PARV-19, we demonstrated the presence of monomeric and oligomeric parvalbumin in all fish analysed, except for gummy shark a cartilaginous fish. Heat processing of this allergen greatly affected its antibody reactivity. While heating caused a reduction in antibody reactivity to multimeric forms of parvalbumins for most bony fish, a complete loss of reactivity was observed for cartilaginous fish. Molecular analysis demonstrated that parvalbumin cross-reactivity, among fish species, is due to the molecular phylogenetic association of this major fish allergen. Copyright © 2013 Elsevier Ltd. All rights reserved.

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.

PubMed

Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L

2018-03-15

Imaging (fluorescence in situ hybridization [FISH]) and genome-wide chromosome conformation capture (Hi-C) are two major approaches to the study of higher-order genome organization in the nucleus. Intra-chromosomal and inter-chromosomal interactions (referred to as non-homologous chromosomal contacts [NHCCs]) have been observed by several FISH-based studies, but locus-specific NHCCs have not been detected by Hi-C. Due to crosslinking, neither of these approaches assesses spatiotemporal properties. Toward resolving the discrepancies between imaging and Hi-C, we sought to understand the spatiotemporal properties of NHCCs in living cells by CRISPR/Cas9 live-cell imaging (CLING). In mammalian cells, we find that NHCCs are stable and occur as frequently as intra-chromosomal interactions, but NHCCs occur at farther spatial distance that could explain their lack of detection in Hi-C. By revealing the spatiotemporal properties in living cells, our study provides fundamental insights into the biology of NHCCs. Copyright © 2018 Elsevier Inc. All rights reserved.

Fish and robots swimming together: attraction towards the robot demands biomimetic locomotion

PubMed Central

Marras, Stefano; Porfiri, Maurizio

2012-01-01

The integration of biomimetic robots in a fish school may enable a better understanding of collective behaviour, offering a new experimental method to test group feedback in response to behavioural modulations of its ‘engineered’ member. Here, we analyse a robotic fish and individual golden shiners (Notemigonus crysoleucas) swimming together in a water tunnel at different flow velocities. We determine the positional preference of fish with respect to the robot, and we study the flow structure using a digital particle image velocimetry system. We find that biomimetic locomotion is a determinant of fish preference as fish are more attracted towards the robot when its tail is beating rather than when it is statically immersed in the water as a ‘dummy’. At specific conditions, the fish hold station behind the robot, which may be due to the hydrodynamic advantage obtained by swimming in the robot's wake. This work makes a compelling case for the need of biomimetic locomotion in promoting robot–animal interactions and it strengthens the hypothesis that biomimetic robots can be used to study and modulate collective animal behaviour. PMID:22356819

Fish and robots swimming together: attraction towards the robot demands biomimetic locomotion.

PubMed

Marras, Stefano; Porfiri, Maurizio

2012-08-07

The integration of biomimetic robots in a fish school may enable a better understanding of collective behaviour, offering a new experimental method to test group feedback in response to behavioural modulations of its 'engineered' member. Here, we analyse a robotic fish and individual golden shiners (Notemigonus crysoleucas) swimming together in a water tunnel at different flow velocities. We determine the positional preference of fish with respect to the robot, and we study the flow structure using a digital particle image velocimetry system. We find that biomimetic locomotion is a determinant of fish preference as fish are more attracted towards the robot when its tail is beating rather than when it is statically immersed in the water as a 'dummy'. At specific conditions, the fish hold station behind the robot, which may be due to the hydrodynamic advantage obtained by swimming in the robot's wake. This work makes a compelling case for the need of biomimetic locomotion in promoting robot-animal interactions and it strengthens the hypothesis that biomimetic robots can be used to study and modulate collective animal behaviour.

Dorso-ventral skin characterization of the farmed fish gilthead seabream (Sparus aurata)

PubMed Central

Cordero, Héctor; Ceballos-Francisco, Diana; Cuesta, Alberto

2017-01-01

The skin is the first barrier of defence in fish, protecting against any external stressor and preserving the integrity and homeostasis of the fish body. The aim of this study was to characterise gilthead seabream skin by isolating cells and studying the cell cycle by flow cytometry, to study the skin histology by scanning electron microscopy and the transcription level of some immune-relevant genes by RT-PCR. Furthermore, the results obtained from samples taken from the dorsal and the ventral part of the specimens are compared. No differences were observed in the cell cycle of cells isolated from the dorsal and ventral zones of the skin or in the gene expression of the genes studied in both epidermal zones. However, the epidermis thickness of the ventral skin was higher than that of the dorsal skin, as demonstrated by image analysis using light microscopy. Besides, scanning electron microscopy pointed to a greater cell size and area of microridges in the apical part of the dorsal epidermal cells compared with ventral skin epidermal cells. This study represents a step forward in our knowledge of the skin structure of an important farmed teleost, gilthead seabream, one of the most commonly farmed fish worldwide. Furthermore, for functional characterization, experimental wounds were carried out comparing the wound healing rate between the dorsal and ventral regions of skin over the time. The results showed higher ratio of wound healing in the ventral region, whose wounds were closed after 15 days, compared to dorsal region of skin. Taking into account all together, this study represents a step forward in our knowledge of the skin structure and skin regeneration of an important farmed teleost, gilthead seabream, one of the most commonly farmed fish worldwide. PMID:28666033

Consumer attitudes and preferences towards pangasius and tilapia: The role of sustainability certification and the country of origin.

PubMed

Hinkes, Cordula; Schulze-Ehlers, Birgit

2018-05-04

The majority of farmed fish produced in Bangladesh is consumed domestically, while global demand for fish is increasing. Non-tariff barriers resulting from consumers' concerns about sustainability and food safety or attitudes towards the country of origin might be one reason for limited export. The purpose of this study is to analyze consumer preferences for frozen pangasius and tilapia fillets from Bangladesh in order to explore market opportunities in Germany. A discrete choice experiment was conducted to estimate marginal utilities and willingness-to-pay for different product attributes, focusing on sustainability certification and the country of origin. Vietnam as a major exporter of pangasius to Germany was selected as a reference country for the analysis. The results of fitted mixed logit models indicate that German consumers are price-sensitive and prefer fish produced in Germany over fish farmed in either Bangladesh or Vietnam. While this finding seems not to be attributable to consumer ethnocentrism, country image constructs might play a role. A significant positive utility was identified for both sustainability and fair trade certification. The overall opt-out rate of the choice experiment was relatively high, indicating a general reluctance to consume pangasius and tilapia. Older respondents as well as those concerned about sustainability and those having less positive attitudes towards aquaculture were more likely to opt out. Overall, concerns about sustainability and the country of origin are relevant factors influencing purchase decisions, but aspects of taste and preferences for certain fish species might be even more significant in this context, limiting the market potential of pangasius and tilapia in Germany. Copyright © 2018 Elsevier Ltd. All rights reserved.

The antiviral innate immune response in fish: evolution and conservation of the IFN system.

PubMed

Langevin, Christelle; Aleksejeva, Elina; Passoni, Gabriella; Palha, Nuno; Levraud, Jean-Pierre; Boudinot, Pierre

2013-12-13

Innate immunity constitutes the first line of the host defense after pathogen invasion. Viruses trigger the expression of interferons (IFNs). These master antiviral cytokines induce in turn a large number of interferon-stimulated genes, which possess diverse effector and regulatory functions. The IFN system is conserved in all tetrapods as well as in fishes, but not in tunicates or in the lancelet, suggesting that it originated in early vertebrates. Viral diseases are an important concern of fish aquaculture, which is why fish viruses and antiviral responses have been studied mostly in species of commercial value, such as salmonids. More recently, there has been an interest in the use of more tractable model fish species, notably the zebrafish. Progress in genomics now makes it possible to get a relatively complete image of the genes involved in innate antiviral responses in fish. In this review, by comparing the IFN system between teleosts and mammals, we will focus on its evolution in vertebrates. © 2013 Elsevier Ltd. All rights reserved.

Automated Reconstruction of Three-Dimensional Fish Motion, Forces, and Torques

PubMed Central

Voesenek, Cees J.; Pieters, Remco P. M.; van Leeuwen, Johan L.

2016-01-01

Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics. PMID:26752597

Flow Behavior Around a Fast-Starting Robotic Fish

NASA Astrophysics Data System (ADS)

Ma, Ganzhong; Currier, Todd; Modarres-Sadeghi, Yahya

2017-11-01

A robotic fish is used to study the flow behavior around the body of a fast-starting fish as it experiences a fast-start. The robotic fish is designed and built emulating a Northern Pike, Esox Lucius, which can accelerate at up to 245 m/s2. In previous studies, we had focused on the flow around the tail during the fast-start, by using a tail which acted flexibly in the preparatory stage and rigidly in the propulsive stage. We have extended that study by including the fish body in the experimental setup, where the body can bend into a C-shape, so that the influence of the body motion on the resulting flow around the structure can be understood as well. In the tests, the fish can rotate about a vertical axis, where a multi-axis force sensor measures flow forces acting on the body. Synchronized with the force measurement, flow visualizations using bubble image velocimetry are conducted, and the observed shed vortices are related to the peak forces observed during the maneuver.

Terahertz imaging for subsurface investigation of art paintings

NASA Astrophysics Data System (ADS)

Locquet, A.; Dong, J.; Melis, M.; Citrin, D. S.

2017-08-01

Terahertz (THz) reflective imaging is applied to the stratigraphic and subsurface investigation of oil paintings, with a focus on the mid-20th century Italian painting, `After Fishing', by Ausonio Tanda. THz frequency-wavelet domain deconvolution, which is an enhanced deconvolution technique combining frequency-domain filtering and stationary wavelet shrinkage, is utilized to resolve the optically thin paint layers or brush strokes. Based on the deconvolved terahertz data, the stratigraphy of the painting including the paint layers is reconstructed and subsurface features are clearly revealed. Specifically, THz C-scans and B-scans are analyzed based on different types of deconvolved signals to investigate the subsurface features of the painting, including the identification of regions with more than one paint layer, the refractive-index difference between paint layers, and the distribution of the paint-layer thickness. In addition, THz images are compared with X-ray images. The THz image of the thickness distribution of the paint exhibits a high degree of correlation with the X-ray transmission image, but THz images also reveal defects in the paperboard that cannot be identified in the X-ray image. Therefore, our results demonstrate that THz imaging can be considered as an effective tool for the stratigraphic and subsurface investigation of art paintings. They also open up the way for the use of non-ionizing THz imaging as a potential substitute for ionizing X-ray analysis in nondestructive evaluation of art paintings.

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay.

PubMed

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Reddy, P Vijay Anand

2012-03-01

Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER 2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated.

Indicators of AEI applied to the Delaware Estuary.

PubMed

Barnthouse, Lawrence W; Heimbuch, Douglas G; Anthony, Vaughn C; Hilborn, Ray W; Myers, Ransom A

2002-05-18

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of "adverse environmental impact" (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community. Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the "BIC" analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the "Trends" analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the "Stock Jeopardy" analysis). The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks. All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.

The utility of fluorescence in situ hybridization for diagnosis and surveillance of bladder urothelial carcinoma.

PubMed

Huang, Jian Wen; Mu, Jia Gui; Li, Yun Wei; Gan, Xiu Guo; Song, Lu Jie; Gu, Bao Jun; Fu, Qiang; Xu, Yue Min; An, Rui Hua

2014-11-30

To evaluate the clinical value of fluorescence in situ hybridization (FISH) for diagnosis and surveillance of bladder urothelial carcinoma (BUC). Between November 2010 and December 2013, patients suspected of having BUC were examined using urine cytology and FISH assay. Based on histopathological examination results, FISH results were com­pared with urine cytology. In addition, patients with a history of non-muscle invasive BUC were also examined using urine cytology and FISH assay at the first time of visit and then monitored with cystoscopy during follow-up period. A total of 162 patients included in this study and 12 patients were excluded due to uninformative FISH assays. The remaining 150 patients consisted of 108 patients suspected for BUC and 42 patients with a history of non-muscle invasive BUC. The sensitivities of FISH analysis and urine cytology were 72.8% and 27.2%, respectively, and the difference was statistically significant (P <.05). Difference between specificity of urine cytology (100%) and FISH assay (85%) was not statistically significant (P >.05). At the first visit, of 42 patients, one patient had positive cystoscopy, and FISH assay was positive in 26 of 41 patients with negative cystoscopy. During the follow-up period (mean, 29.5 months), 18 of 26 patients developed recurrence, and recurrence occurred in only one of 15 patients with negative FISH analysis. Our results suggest that FISH analysis can be used as a non-invasive diagnostic tool for patients suspect­ed of having new BUC. In addition, FISH analysis may provide important prognostic information to better define the individual risk for BUC recurrence.& nbsp;

Feature point based 3D tracking of multiple fish from multi-view images

PubMed Central

Qian, Zhi-Ming

2017-01-01

A feature point based method is proposed for tracking multiple fish in 3D space. First, a simplified representation of the object is realized through construction of two feature point models based on its appearance characteristics. After feature points are classified into occluded and non-occluded types, matching and association are performed, respectively. Finally, the object's motion trajectory in 3D space is obtained through integrating multi-view tracking results. Experimental results show that the proposed method can simultaneously track 3D motion trajectories for up to 10 fish accurately and robustly. PMID:28665966

Feature point based 3D tracking of multiple fish from multi-view images.

PubMed

Qian, Zhi-Ming; Chen, Yan Qiu

2017-01-01

A feature point based method is proposed for tracking multiple fish in 3D space. First, a simplified representation of the object is realized through construction of two feature point models based on its appearance characteristics. After feature points are classified into occluded and non-occluded types, matching and association are performed, respectively. Finally, the object's motion trajectory in 3D space is obtained through integrating multi-view tracking results. Experimental results show that the proposed method can simultaneously track 3D motion trajectories for up to 10 fish accurately and robustly.

Fast detection of Piscirickettsia salmonis in Salmo salar serum through MALDI-TOF-MS profiling.

PubMed

Olate, Verónica R; Nachtigall, Fabiane M; Santos, Leonardo S; Soto, Alex; Araya, Macarena; Oyanedel, Sandra; Díaz, Verónica; Marchant, Vanessa; Rios-Momberg, Mauricio

2016-03-01

Piscirickettsia salmonis is a pathogenic bacteria known as the aetiological agent of the salmonid rickettsial syndrome and causes a high mortality in farmed salmonid fishes. Detection of P. salmonis in farmed fishes is based mainly on molecular biology and immunohistochemistry techniques. These techniques are in most of the cases expensive and time consuming. In the search of new alternatives to detect the presence of P. salmonis in salmonid fishes, this work proposed the use of MALDI-TOF-MS to compare serum protein profiles from Salmo salar fish, including experimentally infected and non-infected fishes using principal component analysis (PCA). Samples were obtained from a controlled bioassay where S. salar was challenged with P. salmonis in a cohabitation model and classified according to the presence or absence of the bacteria by real time PCR analysis. MALDI spectra of the fish serum samples showed differences in its serum protein composition. These differences were corroborated with PCA analysis. The results demonstrated that the use of both MALDI-TOF-MS and PCA represents a useful tool to discriminate the fish status through the analysis of salmonid serum samples. Copyright © 2016 John Wiley & Sons, Ltd.

Iridovirus infections in farm-reared tropical ornamental fish.

PubMed

Paperna, I; Vilenkin, M; de Matos, A P

2001-12-20

A systemic viral infection in both gourami Trichogaster spp. and swordtail Xiphophorus hellerii and an outbreak of lymphocystis in scalare Pterophyllum scalarae and gourami are reported to have occurred in fish reared in ornamental fish farms in Israel. The systemic infection developed in endothelial cells that became hypertrophic and their contents were modified. The presence of such cells in light-microscopically examined stained smears and sections provides an initial indication for this systemic viral infection. Infection in gourami caused hemorrhagic dropsy. Transmission electron microscopic (TEM) images of iridovirus-like particles recovered from gouramies showed them to be 138 to 201 nm from vertex to vertex (v-v); those from swordtails were 170 to 188 nm v-v. TEM images of lymphocystis virions from scalare were 312 to 342 nm v-v and from gourami 292 to 341 nm v-v. Lymphocystis cells from the gourami were joined by a solid hyaline plate, which was lacking in the infection in scalare where the intercellular spaces between the lymphocystis cells consisted of loose connective tissue.

Phytoplankton and sediments in Gulf of Mexico

NASA Technical Reports Server (NTRS)

2002-01-01

Affected both by terrestrial factors like agriculture, deforestation, and erosion, and by marine factors like salinity levels, ocean temperature and water pollution, coastal environments are the dynamic interface between land and sea. In this MODIS image from January 15, 2002, the Gulf of Mexico is awash in a mixture of phytoplankton and sediment. Tan-colored sediment is flowing out into the Gulf from the Mississippi River, whose floodplain cuts a pale, wide swath to the right of center in the image, and also from numerous smaller rivers along the Louisiana coast (center). Mixing with the sediment are the multi-colored blue and green swirls that reveal the presence of large populations of marine plants called phytoplankton. Phytoplankton populations bloom and then fade, and these cycles affect fish and mammals-including humans-higher up the food chain. Certain phytoplankton are toxic to both fish and humans, and coastal health departments must monitor ecosystems carefully, often restricting fishing or harvesting of shellfish until the blooms have subsided.

The host preference and impact of Argulus japonicus ectoparasite on cyprinids in Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Kismiyati; Wulansari, P. D.; Dewi, N. N.

2018-04-01

The most widely cultivated freshwater fish are from Familia Cyprinidae, among others goldfish (Carassius auratus), koi (Cyprinus carpio) and comet goldfish (Carassius auratus auratus). One of the constraints of freshwater fish cultivation is ectoparasite infestation Argulus japonicus. Financial losses have been experienced by some farmers, caused by these ectoparasitic infestaions. This study was aimed to determine the impact of ectoparasite Argulus japonicus infestation on host (freshwater ornamental fish from Familia Cyprinidae), in order to find a preventive solution to treatment on the host. The results showed that prevalence of infested fish by Argulus japonicus were 57 % goldfish, 31 % comet fish and 65 % koi. Changes of histopathology on host were congestion, baoning degeneration, epithelium erosion and inflammatory cell infiltration. The image of infected leukocytes infested by Argulus japonicus were 8.5 % of lymphocytes, 4.7 % neurophils, 3.9 % monocytes, 1.45 % eosinophils and 0,17% basophils.

Markov chain model for demersal fish catch analysis in Indonesia

NASA Astrophysics Data System (ADS)

Firdaniza; Gusriani, N.

2018-03-01

As an archipelagic country, Indonesia has considerable potential fishery resources. One of the fish resources that has high economic value is demersal fish. Demersal fish is a fish with a habitat in the muddy seabed. Demersal fish scattered throughout the Indonesian seas. Demersal fish production in each Indonesia’s Fisheries Management Area (FMA) varies each year. In this paper we have discussed the Markov chain model for demersal fish yield analysis throughout all Indonesia’s Fisheries Management Area. Data of demersal fish catch in every FMA in 2005-2014 was obtained from Directorate of Capture Fisheries. From this data a transition probability matrix is determined by the number of transitions from the catch that lie below the median or above the median. The Markov chain model of demersal fish catch data was an ergodic Markov chain model, so that the limiting probability of the Markov chain model can be determined. The predictive value of demersal fishing yields was obtained by calculating the combination of limiting probability with average catch results below the median and above the median. The results showed that for 2018 and long-term demersal fishing results in most of FMA were below the median value.

Abundance, Fishing Season and Management Strategy for Blue Swimming Crab (Portunus pelagicus) in Pangkajene Kepulauan, South Sulawesi, Indonesia

PubMed Central

Wiyono, Eko Sri; Ihsan

2018-01-01

In order to manage blue swimming crabs in Pangkajene Kepulauan, management measures are required. Since the environment which affects the abundance of the blue swimming crab varies seasonally, it is necessary to take into account the seasonal nature with the aim of developing a management strategy. The objectives of this study are to define the abundance of and fishing season of blue swimming crabs in the Pangkajene Kepulauan waters, South Sulawesi, Indonesia. The fishing season was analysed using seasonal index analysis, while fish abundance was analysed by means of Equilibrium-Schaefer. The result of this study demonstrated that fishermen allocate their fishing gear all year, although the fish catch is seasonal. Based on analysis of the result, the fishing season for the blue swimming crabs is short. The peak fishing season starts in May and finishes in June. However, in order to enable their families to earn a living, fishermen operated their fishing gear throughout the year. As a result, both catch landing and effort were close to maximum sustainable yield (MSY). In order to reduce fishing pressure, it is necessary to reduce fishing gear and have a seasonal arrangement regarding fishing gear allocation. PMID:29644012

Abundance, Fishing Season and Management Strategy for Blue Swimming Crab (Portunus pelagicus) in Pangkajene Kepulauan, South Sulawesi, Indonesia.

PubMed

Wiyono, Eko Sri; Ihsan

2018-03-01

In order to manage blue swimming crabs in Pangkajene Kepulauan, management measures are required. Since the environment which affects the abundance of the blue swimming crab varies seasonally, it is necessary to take into account the seasonal nature with the aim of developing a management strategy. The objectives of this study are to define the abundance of and fishing season of blue swimming crabs in the Pangkajene Kepulauan waters, South Sulawesi, Indonesia. The fishing season was analysed using seasonal index analysis, while fish abundance was analysed by means of Equilibrium-Schaefer. The result of this study demonstrated that fishermen allocate their fishing gear all year, although the fish catch is seasonal. Based on analysis of the result, the fishing season for the blue swimming crabs is short. The peak fishing season starts in May and finishes in June. However, in order to enable their families to earn a living, fishermen operated their fishing gear throughout the year. As a result, both catch landing and effort were close to maximum sustainable yield (MSY). In order to reduce fishing pressure, it is necessary to reduce fishing gear and have a seasonal arrangement regarding fishing gear allocation.

75 FR 81586 - Western Pacific Fishery Management Council; Public Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-28

... spatial closure impacts on the fishing community 2. Guam Fisheries Act 3. Indigenous Fishing Rights 4.... Impact of land-based pollution in fish from Saipan Lagoon 3. Saipan Lagoon net fishing data analysis 4...

A comparison of measures of riverbed form for evaluating distributions of benthic fishes

USGS Publications Warehouse

Wildhaber, Mark L.; Lamberson, Peter J.; Galat, David L.

2003-01-01

A method to quantitatively characterize the bed forms of a large river and a preliminary test of the relationship between bed-form characteristics and catch per unit area of benthic fishes is presented. We used analog paper recordings of bathymetric data from the Missouri River and fish data collected from 1996 to 1998 at both the segment (???101-102-km) and macrohabitat (???10-1-100-km) spatial scales. Bed-form traces were transformed to digital data with image analysis software. The slope, mean residual, and SD of the residuals of the regression of depth versus distance along the bottom, as well as mean depth, were estimated for each trace. These four metrics were compared with sinuosity, fractal dimension, critical scale, and maximum mean angle for the same traces. Mean depth and sinuosity differed among segments and macrohabitats. Fractal-based measures of the relative depth of bottom troughs (critical scale) and smoothness (maximum mean angle) differed among segments. Statistics-based measures of the relative depth of bottom troughs (mean residual) and smoothness (SD of the residuals) differed among macrohabitats. Sites with shovelnose sturgeon Scaphirhynchus platorynchus were shallower and smoother than sites without shovelnose sturgeon. When compared with sites without sicklefin chub Macrhybopsis meeki, sites with sicklefin chub were shallower, had shallower troughs, and sloped more out of the flow of the river. Sites with sturgeon chub M. gelida were shallower, had shallower troughs, and were smoother than sites without sturgeon chub. Sites with and without channel catfish Ictalurus punctatus did not differ for any bed-form variables measured. Nonzero shovelnose sturgeon density increased with depth, whereas nonzero sturgeon chub density decreased with depth. Indices of bed-form structure demonstrated potential for describing the distribution and abundance of Missouri River benthic fishes. The observed fish patterns, though limited, provide valuable direction for future research into the habitat preferences of these fishes.

Formation and oral administration of alginate microspheres loaded with pDNA coding for lymphocystis disease virus (LCDV) to Japanese flounder.

PubMed

Tian, Ji-Yuan; Sun, Xiu-Qin; Chen, Xi-Guang

2008-05-01

Oral delivery of plasmid DNA (pDNA) is a desirable approach for fish immunization in intensive culture. However, its effectiveness is limited because of possible degradation of pDNA in the fish's digestive system. In this report, alginate microspheres loaded with pDNA coding for fish lymphocystis disease virus (LCDV) and green fluorescent protein were prepared with a modified oil containing water (W/O) emulsification method. Yield, loading percent and encapsulation efficiency of alginate microspheres were 90.5%, 1.8% and 92.7%, respectively. The alginate microspheres had diameters of less than 10 microm, and their shape was spherical. As compared to sodium alginate, a remarkable increase of DNA-phosphodiester and DNA-phosphomonoester bonds was observed for alginate microspheres loaded with pDNA by Fourier transform infrared (FTIR) spectroscopic analysis. Agarose gel electrophoresis showed a little supercoiled pDNA was transformed to open circular and linear pDNA during encapsulation. The cumulative release of pDNA in alginate microspheres was or=0.3) for anti-LCDV antibody from week 3 to week 16 for fish orally vaccinated with alginate microspheres loaded with pDNA, in comparison with fish orally vaccinated with naked pDNA. Our results display that alginate microspheres obtained by W/O emulsification are promising carriers for oral delivery of pDNA. This encapsulation technique has the potential for DNA vaccine delivery applications due to its ease of operation, low cost and significant immune effect.

A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients

PubMed Central

Zhong, Qing; Guo, Tiannan; Rechsteiner, Markus; Rüschoff, Jan H.; Rupp, Niels; Fankhauser, Christian; Saba, Karim; Mortezavi, Ashkan; Poyet, Cédric; Hermanns, Thomas; Zhu, Yi; Moch, Holger; Aebersold, Ruedi; Wild, Peter J.

2017-01-01

Microscopy image data of human cancers provide detailed phenotypes of spatially and morphologically intact tissues at single-cell resolution, thus complementing large-scale molecular analyses, e.g., next generation sequencing or proteomic profiling. Here we describe a high-resolution tissue microarray (TMA) image dataset from a cohort of 71 prostate tissue samples, which was hybridized with bright-field dual colour chromogenic and silver in situ hybridization probes for the tumour suppressor gene PTEN. These tissue samples were digitized and supplemented with expert annotations, clinical information, statistical models of PTEN genetic status, and computer source codes. For validation, we constructed an additional TMA dataset for 424 prostate tissues, hybridized with FISH probes for PTEN, and performed survival analysis on a subset of 339 radical prostatectomy specimens with overall, disease-specific and recurrence-free survival (maximum 167 months). For application, we further produced 6,036 image patches derived from two whole slides. Our curated collection of prostate cancer data sets provides reuse potential for both biomedical and computational studies. PMID:28291248

Target-induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs.

PubMed

Xue, Chang; Zhang, Shu-Xin; Ouyang, Chang-He; Chang, Dingran; Salena, Bruno J; Li, Yingfu; Wu, Zai-Sheng

2018-06-14

DNA is a highly programmable material that can be configured into unique high-order structures, such as DNA branched junctions containing multiple helical arms converging at a center. Herein we show that DNA programmability can deliver in situ growth of a 3-way junction-based DNA structure (denoted Y-shaped DNA) with the use of three hairpin-shaped DNA molecules as precursors, a specific microRNA target as a recyclable trigger, and a DNA polymerase as a driver. We demonstrate that the Y-shaped configuration comes with the benefit of restricted freedom of movement in confined cellular environment, which makes the approach ideally suited for in situ imaging of small RNA targets, such as microRNAs. Comparative analysis illustrates that the proposed imaging technique is superior to both the classic fluorescence in situ hybridization (FISH) method and an analogous amplified imaging method via programmed growth of a double-stranded DNA (rather than Y-shaped DNA) product. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trophic characteristics of a mangrove fish community in Southwest Thailand: Important mangrove contribution and intraspecies feeding variability

NASA Astrophysics Data System (ADS)

Zagars, Matiss; Ikejima, Kou; Kasai, Akihide; Arai, Nobuaki; Tongnunui, Prasert

2013-03-01

Mangrove production has been found to make a major contribution to the nutrition of a fish community in the Sikao Creek mangrove estuary, Southwest Thailand. Gut content analysis and carbon and nitrogen stable isotope analysis were used to assess fish feeding behavior and trophic reliance on different primary producers (mangrove leaves, phytoplankton, microphytobenthos) focusing on 19 dominant fish species, and 4 potential fish food items. Cluster analysis identified 5 trophic groups and the IsoSource model indicated the importance of primary food sources in trophically supporting different fish species. Most analyzed fish species had carbon isotopic signatures that were more depleted than those reported in previous studies, and the IsoSource model indicated that mangrove leaves were an important primary food source. This may be a specific characteristic of our study site, which is not well connected to other productive coastal habitats that provide alternative primary food sources. Thus we suggest that food chains in trophically isolated mangrove estuaries of southwest Thailand are more dependent on mangrove tree production. We also assessed the relationship of individuality in fish feeding habits and variability of δ13C values and showed that several mangrove fish species have significant intraspecies variability in feeding habits, possibly due to high intraspecific competition.

Fish consumption in a sample of people in Bandar Abbas, Iran: application of the theory of planned behavior.

PubMed

Aghamolaei, Teamur; Sadat Tavafian, Sedigheh; Madani, Abdoulhossain

2012-09-01

This study aimed to apply the conceptual framework of the theory of planned behavior (TPB) to explain fish consumption in a sample of people who lived in Bandar Abbass, Iran. We investigated the role of three traditional constructs of TPB that included attitude, social norms, and perceived behavioral control in an effort to characterize the intention to consume fish as well as the behavioral trends that characterize fish consumption. Data were derived from a cross-sectional sample of 321 subjects. Alpha coefficient correlation and linear regression analysis were applied to test the relationships between constructs. The predictors of fish consumption frequency were also evaluated. Multiple regression analysis revealed that attitude, subjective norms, and perceived behavioral control significantly predicted intention to eat fish (R2 = 0.54, F = 128.4, P < 0.001). Multiple regression analysis for the intention to eat fish and perceived behavioral control revealed that both factors significantly predicted fish consumption frequency (R2 = 0.58, F = 223.1, P < 0.001). The results indicated that the models fit well with the data. Attitude, subjective norms, and perceived behavioral control all had significant positive impacts on behavioral intention. Moreover, both intention and perceived behavioral control could be used to predict the frequency of fish consumption.

The use of archived tags in retrospective genetic analysis of fish.

PubMed

Bonanomi, Sara; Therkildsen, Nina Overgaard; Hedeholm, Rasmus Berg; Hemmer-Hansen, Jakob; Nielsen, Einar E

2014-05-01

Collections of historical tissue samples from fish (e.g. scales and otoliths) stored in museums and fisheries institutions are precious sources of DNA for conducting retrospective genetic analysis. However, in some cases, only external tags used for documentation of spatial dynamics of fish populations have been preserved. Here, we test the usefulness of fish tags as a source of DNA for genetic analysis. We extract DNA from historical tags from cod collected in Greenlandic waters between 1950 and 1968. We show that the quantity and quality of DNA recovered from tags is comparable to DNA from archived otoliths from the same individuals. Surprisingly, levels of cross-contamination do not seem to be significantly higher in DNA from external (tag) than internal (otolith) sources. Our study therefore demonstrates that historical tags can be a highly valuable source of DNA for retrospective genetic analysis of fish. © 2013 John Wiley & Sons Ltd.

The Modular Optical Underwater Survey System

PubMed Central

Amin, Ruhul; Richards, Benjamin L.; Misa, William F. X. E.; Taylor, Jeremy C.; Miller, Dianna R.; Rollo, Audrey K.; Demarke, Christopher; Ossolinski, Justin E.; Reardon, Russell T.; Koyanagi, Kyle H.

2017-01-01

The Pacific Islands Fisheries Science Center deploys the Modular Optical Underwater Survey System (MOUSS) to estimate the species-specific, size-structured abundance of commercially-important fish species in Hawaii and the Pacific Islands. The MOUSS is an autonomous stereo-video camera system designed for the in situ visual sampling of fish assemblages. This system is rated to 500 m and its low-light, stereo-video cameras enable identification, counting, and sizing of individuals at a range of 0.5–10 m. The modular nature of MOUSS allows for the efficient and cost-effective use of various imaging sensors, power systems, and deployment platforms. The MOUSS is in use for surveys in Hawaii, the Gulf of Mexico, and Southern California. In Hawaiian waters, the system can effectively identify individuals to a depth of 250 m using only ambient light. In this paper, we describe the MOUSS’s application in fisheries research, including the design, calibration, analysis techniques, and deployment mechanism. PMID:29019962

Fishery research in the Great Lakes using a low-cost remotely operated vehicle

USGS Publications Warehouse

Kennedy, Gregory W.; Brown, Charles L.; Argyle, Ray L.

1988-01-01

We used a MiniROVER MK II remotely operated vehicle (ROV) to collect ground-truth information on fish and their habitat in the Great Lakes that have traditionally been collected by divers, or with static cameras, or submersibles. The ROV, powered by 4 thrusters and controlled by the pilot at the surface, was portable and efficient to operate throughout the Great Lakes in 1987, and collected a total of 30 h of video data recorded for later analysis. We collected 50% more substrate information per unit of effort with the ROV than with static cameras. Fish behavior ranged from no avoidance reaction in ambient light, to erratic responses in the vehicle lights. The ROV's field of view depended on the time of day, light levels, and density of zooplankton. Quantification of the data collected with the ROV (either physical samples or video image data) will serve to enhance the use of the ROV as a research tool to conduct fishery research on the Great Lakes.

A multifaceted FISH approach to study endogenous RNAs and DNAs in native nuclear and cell structures.

PubMed

Byron, Meg; Hall, Lisa L; Lawrence, Jeanne B

2013-01-01

Fluorescence in situ hybridization (FISH) is not a singular technique, but a battery of powerful and versatile tools for examining the distribution of endogenous genes and RNAs in precise context with each other and in relation to specific proteins or cell structures. This unit offers the details of highly sensitive and successful protocols that were initially developed largely in our lab and honed over a number of years. Our emphasis is on analysis of nuclear RNAs and DNA to address specific biological questions about nuclear structure, pre-mRNA metabolism, or the role of noncoding RNAs; however, cytoplasmic RNA detection is also discussed. Multifaceted molecular cytological approaches bring precise resolution and sensitive multicolor detection to illuminate the organization and functional roles of endogenous genes and their RNAs within the native structure of fixed cells. Solutions to several common technical pitfalls are discussed, as are cautions regarding the judicious use of digital imaging and the rigors of analyzing and interpreting complex molecular cytological results.

Development of new family of wide-angle anamorphic lens with controlled distortion profile

NASA Astrophysics Data System (ADS)

Gauvin, Jonny; Doucet, Michel; Wang, Min; Thibault, Simon; Blanc, Benjamin

2005-08-01

It is well known that a fish-eye lens produces a circular image of the scene with a particular distortion profile. When using a fish-eye lens with a standard sensor (e.g. 1/3", 1/4",.), only a part of the rectangular detector area is used, leaving many pixels unused. We proposed a new approach to get enhanced resolution for panoramic imaging. In this paper, various arrangements of innovative 180-degree anamorphic wide-angle lens design are considered. Their performances as well as lens manufacturability are also discussed. The concept of the design is to use anamorphic optics to produce elliptical image that maximize pixel resolution in both axis. Furthermore, a non-linear distortion profile is also introduced to enhance spatial resolution for specific field angle. Typical applications such as panoramic photography, video conferencing, and homeland/transportation security are also presented.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Copeland, Timothy; Putnam, Scott

The goal of Idaho Steelhead Monitoring and Evaluation Studies is to collect monitoring data to evaluate wild and natural steelhead populations in the Clearwater and Salmon river drainages. During 2007, intensive population data were collected in Fish Creek (Lochsa River tributary) and Rapid River (Little Salmon River tributary); extensive data were collected in other selected spawning tributaries. Weirs were operated in Fish Creek and Rapid River to estimate adult escapement and to collect samples for age determination and genetic analysis. Snorkel surveys were conducted in Fish Creek, Rapid River, and Boulder Creek (Little Salmon River tributary) to estimate parr density.more » Screw traps were operated in Fish Creek, Rapid River, Secesh River, and Big Creek to estimate juvenile emigrant abundance, to tag fish for survival estimation, and to collect samples for age determination and genetic analysis. The estimated wild adult steelhead escapement in Fish Creek was 81 fish and in Rapid River was 32 fish. We estimate that juvenile emigration was 24,127 fish from Fish Creek; 5,632 fish from Rapid River; and 43,674 fish from Big Creek. The Secesh trap was pulled for an extended period due to wildfires, so we did not estimate emigrant abundance for that location. In cooperation with Idaho Supplementation Studies, trap tenders PIT tagged 25,618 steelhead juveniles at 18 screw trap sites in the Clearwater and Salmon river drainages. To estimate age composition, 143 adult steelhead and 5,082 juvenile steelhead scale samples were collected. At the time of this report, 114 adult and 1,642 juvenile samples have been aged. Project personnel collected genetic samples from 122 adults and 839 juveniles. We sent 678 genetic samples to the IDFG Eagle Fish Genetics Laboratory for analysis. Water temperature was recorded at 37 locations in the Clearwater and Salmon river drainages.« less

Calculation of pressure drop in the developmental stages of the medaka fish heart and microvasculature

NASA Astrophysics Data System (ADS)

Chakraborty, Sreyashi; Vlachos, Pavlos

2016-11-01

Peristaltic contraction of the developing medaka fish heart produces temporally and spatially varying pressure drop across the atrioventricular (AV) canal. Blood flowing through the tail vessels experience a slug flow across the developmental stages. We have performed a series of live imaging experiments over 14 days post fertilization (dpf) of the medaka fish egg and cross-correlated the red blood cell (RBC) pattern intensities to obtain the two-dimensional velocity fields. Subsequently we have calculated the pressure field by integrating the pressure gradient in the momentum equation. Our calculations show that the pressure drop across the AV canal increases from 0.8mm Hg during 3dpf to 2.8 mm Hg during 14dpf. We have calculated the time-varying wall shear stress for the blood vessels by assuming a spatially constant velocity magnitude in each vessel. The calculated wall shear stress matches the wall shear stress sensed by human endothelial cells (10-12 dyne/sq. cm). The pressure drop per unit length of the vessel is obtained by doing a control volume analysis of flow in the caudal arteries and veins. The current results can be extended to investigate the effect of the fluid dynamic parameters on the vascular and cardiac morphogenesis.

Isolation and Characterization of Prostate Cancer Stem Cells

DTIC Science & Technology

2011-08-01

and ability to induce prostate tubule formation in vivo. FISH analysis of prostaspheres derived from patient specimens containing the TMPRSS-ERG...hybridization (FISH)[6]. Analysis of prostate tumor surgical cohorts have found 36-78% of prostate cancers possess the TMPRSS-ERG fusion[6]. We wondered...suggest that cancer stem/early progenitor cells can be expanded in our cultures. 6 To test the feasibility of this approach, FISH analysis was

Analysis of EPA and DHA in the viscera of marine fish using gas chromatography.

PubMed

Zhang, De-Yong; Xu, Xiao-Lu; Shen, Xiu-Ying; Mei, Yu; Xu, Hui-Ying

2016-03-01

The viscera of 10 kinds of marine fishes were collected for fish oil extraction and detection of DHA and EPA, two most important polyunsaturated fatty acids. The fish oil extraction ratio for the evaluated fishes varied from 0.95% to 10.18% (wt%). Pseudosciaena crocea presented the highest fish oil yield, followed by Mustelus manazo, Hippoglossus and Sciaenopsocellatus. A gas chromatography method was then established for analysis of EPA/DHA. The EPA concentration (in methyl ester form) in the fish oil varied from 1.39 to 10.65(mg/g). Epinephelus awoara presented the highest EPA concentration (p<0.05), followed by Epinephelussp, Sciaenopsocellatus and Hippoglossus. The DHA concentration (in methyl ester form) in the fish oil varied from 0.58 to 37.02 (mg/g). Epinephelus awoara presented the highest DHA concentration (p<0.05), followed by Sciaenopsocellatus, Pseudosciaena crocea and Hippoglossus. No strict positive correlation between the EPA/DHA concentration and the sea depth where the fish live was observed. The fishes living in middle depth presented highest EPA/DHA concentration.

Analysis of occupational injuries in the sea fishing industry according to the type of fishery and the fishing activity.

PubMed

Chauvin, Christine; Le Bouar, Gilbert; Lardjane, Salim

2017-01-01

Sea fishing is one of the most dangerous occupations. Numerous studies have already sought to evaluate the risk level of this occupation through the analysis of the frequency and seriousness of occupational injuries. The purpose of the present study is to analyse these accidents in terms of two main characteristics of the vessels involved: the fishery type (high seas, offshore, coastal, or inshore fishery) and the fishing activity (use of passive or active gears). Injury rates were calculated for the Brittany region and for the year 2012. A second analysis was carried out on 8,286 reported injuries that occurred in France from 2002 to 2012, while vessels were in the process of fishing. This first analysis shows that the incidence rate is very high (103 per 1,000 full-time equivalent fishermen) and that it depends more on the fishery type than on the fishing activity; the highest rates concern the offshore and the coastal fleets. Results of the second analysis show that the nature of accidents depends more on the fishing activity than on the type of fishery. These findings lead to a discussion of the causes of the highest incidence rate values and the causes of the observed variations. The discussion also involves the methodological difficulties related to the incidence rate calculations.

Application of remote sensing for fishery resources assessment and monitoring. [Gulf of Mexico

NASA Technical Reports Server (NTRS)

Savastano, K. J. (Principal Investigator)

1975-01-01

The author has identified the following significant results. The distribution and abundance of white marlin correlated with the chlorophyll, water temperature, and Secchi depth sea truth measurements. Results of correlation analyses for dolphin were inconclusive. Predicition models for white marlin were developed using stepwise multiple regression and discriminant function analysis techniques which demonstrated a potential for increasing the probability of game fishing success. The S190A and B imagery was density sliced/color enhanced with white marlin location superimposed on the image, but no density/white marlin relationship could be established.

Scombrotoxic fish poisoning in Britain: features of over 250 suspected incidents from 1976 to 1986.

PubMed Central

Bartholomew, B. A.; Berry, P. R.; Rodhouse, J. C.; Gilbert, R. J.; Murray, C. K.

1987-01-01

Between 1976 and 1986, 258 incidents of suspected scombrotoxic fish poisoning were reported in Britain. Histamine analysis was carried out on 240 fish samples from these incidents, and 101 were found to contain greater than 5 mg histamine/100 g fish. The symptoms most consistently reported were rash, diarrhoea, flushing and headache. In recent years there has been a decrease in the number of confirmed scombrotoxic outbreaks and a trend towards more sporadic incidents. Of fish samples with greater than 20 mg histamine/100 g, 94% were from incidents in which scombrotoxic symptoms were characteristic, but where fish had 5-20 mg/100 g only 38% of incidents were clinically distinctive. Guidelines are presented based on the interpretation of quantitative histamine analysis of fish samples from scombrotoxic poisoning incidents. PMID:3428380

A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

USGS Publications Warehouse

Adams, Noah S.; Hatton, Tyson W.

2012-01-01

Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the dam. In comparison, greater than 0.20 of the Chinook salmon passed within the powerhouse areas. Less milling behavior was observed for all species for fish that first approached the spillway. Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and fewer transitioned to adjoining areas in the powerhouse. In addition to quantifying what had been previously speculated about the behavior of fish in the forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and passage can be influenced by changes to the operations and structure of McNary Dam. For example, the addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been reported showing that TSWs increased the number of fish passing through non-turbine routes and the fish-track videos indicated, in general, how fish behaved before passing through the TSWs. However, the analysis presented in this report allowed us to better understand how fish moved across the face of the dam before passing the TSWs and provided a way to quantify the effect of TSW location. Installation of the TSWs in bays 22 and 20 clearly increased passage proportions through the southern one-third of the spillway area for all species, most significantly for steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007. Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased the number of fish that moved to adjoining areas before passing the dam. Perhaps the most interesting new information to come out of the two-step Markov chain analysis relates to how the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the highest proportion of fish passing through TSW22 was for fish that transitioned from the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW20 after coming from the powerhouse area. Instead, the proportion of fish that passed TSW20 after coming from the northern part of the spillway was twice as high as the proportion of fish that passed through TSW20 after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 22; the proportion of fish passing TSW20 after coming from the powerhouse was greater than the proportion of fish passing through TSW20 after coming from the northern part of the spillway. Passage proportions for fish passing through TSW19, the farthest north of the two TSWs during 2008, was higher for fish that came from the northern part of the spillway compared to the proportion of fish that passed through TSW19 after coming from the powerhouse. The Markov chain analysis provided a mathematical way to characterize fish behavior in the forebay of McNary Dam and helped refine our understanding of how fish movements were influenced by operational and structural changes at McNary Dam. The Markov chain analysis also could be used to examine how future structural and operational changes proposed for McNary Dam might influence the passage of juvenile salmonids.

Managing for desired experiences and site preferences: the case of fee-fishing anglers.

PubMed

Schuett, Michael A; Pierskalla, Chad D

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia (n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.

Managing for Desired Experiences and Site Preferences: The Case of Fee-Fishing Anglers

NASA Astrophysics Data System (ADS)

Schuett, Michael A.; Pierskalla, Chad D.

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia ( n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

PubMed Central

2010-01-01

Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals. PMID:20707909

Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha).

PubMed

Ford, Michael J; Murdoch, Andrew; Hughes, Michael

2015-03-01

We used parentage analysis based on microsatellite genotypes to measure rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha) among five major spawning tributaries within the Wenatchee River, Washington. On the basis of analysis of 2248 natural-origin and 11594 hatchery-origin fish, we estimated that the rate of homing to natal tributaries by natural-origin fish ranged from 0% to 99% depending on the tributary. Hatchery-origin fish released in one of the five tributaries homed to that tributary at a far lower rate than the natural-origin fish (71% compared to 96%). For hatchery-released fish, stray rates based on parentage analysis were consistent with rates estimated using physical tag recoveries. Stray rates among major spawning tributaries were generally higher than stray rates of tagged fish to areas outside of the Wenatchee River watershed. Within the Wenatchee watershed, rates of straying by natural-origin fish were significantly affected by spawning tributary and by parental origin: progeny of naturally spawning hatchery-produced fish strayed at significantly higher rates than progeny whose parents were themselves of natural origin. Notably, none of the 170 offspring that were products of mating by two natural-origin fish strayed from their natal tributary. Indirect estimates of gene flow based on FST statistics were correlated with but higher than the estimates from the parentage data. Tributary-specific estimates of effective population size were also correlated with the number of spawners in each tributary. Published [2015]. This article is a U.S. Government work and is in the public domain in the USA.

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay

PubMed Central

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Vijay, Anand Reddy P.

2012-01-01

Background & objectives: Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. Methods: A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Results: Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Interpretation & conclusions: Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated. PMID:22561616

Biochemical effects of commercial feedstuffs on the fry of climbing perch (Anabas testudineus) and its impact on Swiss albino mice as an animal model.

PubMed

Munshi, Mita; Tumu, Khairun Nafiz; Hasan, Md Nazmul; Amin, Md Ziaul

2018-01-01

This study assesses the biochemical effects of commercially available fish feedstuffs on the fry of climbing perch ( Anabas testudineus ). Subsequently, its impact on experimental animal, Swiss albino mice, is also examined. In order to access the impact of commercial fish feed and feed consumption fish on the experimental animal, the proximate, biochemical and histopathological analyses were done using standard methods. The proximate composition as well as the concentrations of Pb, Ni, Mn, As, Zn, and Cd in the fish feed, different parts of the A. testudineus fish and different parts of the A. testudineus fish-treated experimental mice liver, were all determined using Energy Dispersive X-ray Fluorescence (EDXRF) Spectrometry. The highest levels of Cr, Pb and As were observed in the liver of Swiss albino mice treated with FFT2 and FFBB2 and their concentrations were 0.156, 0.491, 0.172 μg/g and 0.166, 0.771, 0.157 μg/g respectively. No significant changes of protein, fat, crude fiber, moisture and ash contents were observed after proximate composition analysis of fish feeds, A. testudineus and A. testudineus treated experimental mice. Significant amounts of heavy metals (Cr, Mn, Zn Cu, Ni) were found in fish feed, different parts of A. testudineus fish and in the experimental mice. However, remarkably high amounts were observed in the A. testudineus fish's head and bone with body parts. Biochemical analysis of blood samples of A. testudineus fish treated experimental mice indicated that the cholesterol, TG, LDL and glucose levels were significantly higher. Yet no significant alteration in the HDL level was observed when compared to the control. In histopathological analysis, a remarkable degeneration was observed in the liver and kidney of A. testudineus treated mice. It can therefore be concluded that although A. testudineus has nutritional benefits the quality of this fish may be compromised as a consequence of contamination through various anthropogenic activities. This analysis suggests the commercial fish feed producers must take special caution to reduce the toxic metals in various fish feed products and make it nutritionally rich and safe for fish to eat. Finally, it needs to be safe for human consumption as well.

Analysis of Trends in Fish Assemblages in Narragansett Bay, RI/MA

EPA Science Inventory

Estuarine fish are highly valued resources that are affected by several factors, including climate, landscape, pollution, and fishing pressure. Here, we examine patterns of variability in estuarine fish assemblages in Narragansett Bay, an estuary located in Rhode Island and Mass...

3D tooth microwear texture analysis in fishes as a test of dietary hypotheses of durophagy

NASA Astrophysics Data System (ADS)

Purnell, Mark A.; Darras, Laurent P. G.

2016-03-01

An understanding of how extinct animals functioned underpins our understanding of past evolutionary events, including adaptive radiations, and the role of functional innovation and adaptation as drivers of both micro- and macroevolution. Yet analysis of function in extinct animals is fraught with difficulty. Hypotheses that interpret molariform teeth in fishes as evidence of durophagous (shell-crushing) diets provide a good example of the particular problems inherent in the methods of functional morphology. This is because the assumed close coupling of form and function upon which the approach is based is weakened by, among other things, behavioural flexibility and the absence of a clear one to one relationship between structures and functions. Here we show that ISO 25178-2 standard parameters for surface texture, derived from analysis of worn surfaces of molariform teeth of fishes, vary significantly between species that differ in the amount of hard-shelled prey they consume. Two populations of the Sheepshead Seabream (Archosargus probatocephalus) were studied. This fish is not a dietary specialist, and one of the populations is known to consume more vegetation and less hard-shelled prey than the other; this is reflected in significant differences in their microwear textures. The Archosargus populations differ significantly in their microwear from the specialist shell-crusher Anarhichas lupus (the Atlantic Wolffish). Multivariate analysis of these three groups of fishes lends further support to the relationship between diet and tooth microwear, and provides robust validation of the approach. Application of the multivariate models derived from microwear texture in Archosargus and Anarhichas to a third fish species—the cichlid Astatoreochromis alluaudi—successfully separates wild caught fish that ate hard-shelled prey from lab-raised fish that did not. This cross-taxon validation demonstrates that quantitative analysis of tooth microwear texture can differentiate between fishes with different diets even when they range widely in size, habitat, and in the structure of their trophic apparatus. The approach thus has great potential as an additional tool for dietary analysis in extant fishes, and for testing dietary hypotheses in ancient and extinct species.

The role of immunohistochemical analysis in the evaluation of EML4-ALK gene rearrangement in lung cancer.

PubMed

Sullivan, Harold C; Fisher, Kevin E; Hoffa, Anne L; Wang, Jason; Saxe, Debra; Siddiqui, Momin T; Cohen, Cynthia

2015-04-01

Among the mutations described in non-small cell lung carcinoma is a rearrangement resulting from an inversion within chromosome 2p leading to the formation of a fusion gene, echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK). Fluorescence in situ hybridization (FISH) is the gold standard for the detection of ALK gene rearrangements. However, molecular methods are not readily available in all pathology laboratories. Immunohistochemistry (IHC) using an antibody directed against the EML4-ALK fusion protein provides a widely available alternative method of detection. We assessed whether IHC is a comparable and cost-effective alternative to FISH analysis for the detection of ALK gene rearrangements. A total of 110 non-small cell lung carcinoma cases (63 surgical/biopsy and 47 cytology specimens), previously tested for ALK gene rearrangements by FISH [7 (6.4%) positive for the rearrangement], were probed for the EML4-ALK fusion protein using a monoclonal EML4-ALK antibody, clone 5A4. Cells were considered to stain positive for ALK if >5% of cells showed cytoplasmic staining of at least grade 1 intensity (scale: 0 to 3). A cost analysis was performed using ALK IHC as a screening test. The sensitivity and specificity of the EML4-ALK IHC stain compared with ALK FISH analysis were 100% and 96%, respectively. All 7 FISH-positive cases stained positive by IHC, whereas 4 FISH-negative cases demonstrated positive staining. One of the 4 FISH-negative, IHC-positive cases harbored an EML4-ALK rearrangement by RT-PCR yielding 3 false-positive results overall. The κ agreement between IHC and FISH methods is 0.76 (substantial/excellent). The potential savings of implementing the ALK IHC as a screening method would be $10,418.21. Sensitivity of the EML4-ALK IHC stain is excellent (100%) but due to its suboptimal specificity, IHC cannot reliably supplant FISH analysis for the detection of ALK gene rearrangements. IHC shows promise as a screening tool to prevent unnecessary costly FISH analysis.

High-throughput physical mapping of chromosomes using automated in situ hybridization.

PubMed

George, Phillip; Sharakhova, Maria V; Sharakhov, Igor V

2012-06-28

Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila, allows the user to visualize more details on chromosomes than the regular squashing technique. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

A Fisheries Application of a Dual-Frequency Identification Sonar Acoustic Camera

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moursund, Russell A.; Carlson, Thomas J.; Peters, Rock D.

2003-06-01

The uses of an acoustic camera in fish passage research at hydropower facilities are being explored by the U.S. Army Corps of Engineers. The Dual-Frequency Identification Sonar (DIDSON) is a high-resolution imaging sonar that obtains near video-quality images for the identification of objects underwater. Developed originally for the Navy by the University of Washington?s Applied Physics Laboratory, it bridges the gap between existing fisheries assessment sonar and optical systems. Traditional fisheries assessment sonars detect targets at long ranges but cannot record the shape of targets. The images within 12 m of this acoustic camera are so clear that one canmore » see fish undulating as they swim and can tell the head from the tail in otherwise zero-visibility water. In the 1.8 MHz high-frequency mode, this system is composed of 96 beams over a 29-degree field of view. This high resolution and a fast frame rate allow the acoustic camera to produce near video-quality images of objects through time. This technology redefines many of the traditional limitations of sonar for fisheries and aquatic ecology. Images can be taken of fish in confined spaces, close to structural or surface boundaries, and in the presence of entrained air. The targets themselves can be visualized in real time. The DIDSON can be used where conventional underwater cameras would be limited in sampling range to < 1 m by low light levels and high turbidity, and where traditional sonar would be limited by the confined sample volume. Results of recent testing at The Dalles Dam, on the lower Columbia River in Oregon, USA, are shown.« less

Risk factors for Clonorchis sinensis infection transmission in humans in northern Vietnam: A descriptive and social network analysis study.

PubMed

Vinh, Hoang Quang; Phimpraphai, Waraphon; Tangkawattana, Sirikachorn; Smith, John F; Kaewkes, Sasithorn; Dung, Do Trung; Duong, Tran Thanh; Sripa, Banchob

2017-04-01

Clonorchis sinensis is major fish-borne trematode, endemic in North Vietnam. Risk factors described so far include individual eating behaviors and environmental factors. Here, additional to conventional risk factors, we report on socially influenced liver fluke transmission in endemic communities. A cross-sectional study on risk factors and fish sharing networks was conducted in 4 villages of Gia Thinh Commune, Ninh Binh Province. A total of 510 residents in 272 households were recruited for risk factor analysis while 220 households, 28 fishermen and 10 fish-sellers were enrolled for social network study. Fecal examination for C. sinensis eggs was performed. Average C. sinensis infection rate at Gia Thinh commune was 16.5% (range 2% to 34.4%). Higher infection rates were significantly associated with males, lower educational levels, eating raw fish, and location of the villages. Social network analysis (SNA) showed a strong positive correlation between ego network size (number of households in fish sharing network) and quantity of raw fish consumed (r=0.603, P<0.05). The infection rate in people who ate raw-fish caught from a nearby river was significantly higher than those who consumed fish taken from farmed ponds (P<0.05). The amount of raw-fish meal consumed per resident/year was significantly higher in villages that had a strong network of sharing raw-fish food (P<0.001). This study reports for the first time on fish-food sharing among neighbors, proximity to water bodies, frequency of eating raw fish from natural water bodies and low education were key risk factors in C. sinensis infection transmission in northern Vietnam. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Risk factors for Clonorchis sinensis infection transmission in humans in northern Vietnam: A descriptive and social network analysis study

PubMed Central

Vinh, Hoang Quang; Phimpraphai, Waraphon; Tangkawattana, Sirikachorn; Smith, John F.; Kaewkes, Sasithorn; Dung, Do Trung; Duong, Tran Thanh; Sripa, Banchob

2016-01-01

Clonorchis sinensis is major fish-borne trematode, endemic in North Vietnam. Risk factors described so far include individual eating behaviors and environmental factors. Here, additional to conventional risk factors, we report on socially influenced liver fluke transmission in endemic communities. A cross-sectional study on risk factors and fish sharing networks was conducted in 4 villages of Gia Thinh Commune, Ninh Binh Province. A total of 510 residents in 272 households were recruited for risk factor analysis while 220 households, 28 fishermen and 10 fish-sellers were enrolled for social network study. Fecal examination for C. sinensis eggs was performed. Average C. sinensis infection rate at Gia Thinh commune was 16.5% (range 2% to 34.4%). Higher infection rates were significantly associated with males, lower educational levels, eating raw fish, and location of the villages. Social network analysis (SNA) showed a strong positive correlation between ego network size (number of households in fish sharing network) and quantity of raw fish consumed (r=0.603, P< 0.05). The infection rate in people who ate raw-fish caught from a nearby river was significantly higher than those who consumed fish taken from farmed ponds (P<0.05). The amount of raw-fish meal consumed per resident/year was significantly higher in villages that had a strong network of sharing raw-fish food (P<0.001). This study reports for the first time on fish-food sharing among neighbors, proximity to water bodies, frequency of eating raw fish from natural water bodies and low education were key risk factors in C. sinensis infection transmission in northern Vietnam. PMID:27939296

Limnological study with reference to fish culture of Bothali (Mendha) reservoir, district - Gadchiroli (India).

PubMed

Tijare, Rajendra V

2012-04-01

Limnological study with reference to fish culture was carried out at Bothali (Mendha) reservoir, district Gadchiroli, India. Water samples from different sampling locations were collected and processed for physico-chemical analysis. The physico-chemical analysis revealed that the reservoir is favourable for fish culture as the phosphate content in water is moderate in amount. This reservoir can produce a good yield of fishes. Though the reservoir is presently exploited and is under pisciculture, a better treatment of the reservoir such as prevention of entry of organic matter, reduction of phosphate ion concentration to certain extent is necessary to obtain a maximum fish yield.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Zhiqun; Richmond, Marshall C.; Guensch, Gregory R.

Existing literature of previous particle image velocimetry (PIV) studies of fish swimming has been reviewed. Historically, most of the studies focused on the performance evaluation of freely swimming fish. Technological advances over the last decade, especially the development of digital particle image velocimetry (DPIV) technique, make possible more accurate, quantitative descriptions of the flow patterns adjacent to the fish and in the wake behind the fins and tail, which are imperative to decode the mechanisms of drag reduction and propulsive efficiency. For flows generated by different organisms, the related scales and flow regimes vary significantly. For small Reynolds numbers, viscositymore » dominates; for very high Reynolds numbers, inertia dominates, and three-dimensional complexity occurs. The majority of previous investigations dealt with the lower end of Reynolds number range. The fish of our interest, such as rainbow trout and spring and fall chinook salmon, fall into the middle range, in which neither viscosity nor inertia is negligible, and three-dimensionality has yet to dominate. Feasibility tests have proven the applicability of PIV to flows around fish. These tests have shown unsteady vortex shedding in the wake, high vorticity region and high stress region, with the highest in the pectoral area. This evident supports the observations by Nietzel et al. (2000) and Deng et al. (2004) that the operculum are most vulnerable to damage from the turbulent shear flow, because they are easily pried open, and the large vorticity and shear stress can lift and tear off scales, rupture or dislodge eyes, and damage gills. In addition, the unsteady behavior of the vortex shedding in the wake implies that injury to fish by the instantaneous flow structures would likely be much higher than the injury level estimated using the average values of the dynamics parameters. Based on existing literature, our technological capability, and relevance and practicability to Department of Energy's Hydropower Program, we identified three major research areas of interest: free swimming, the boundary layer over fish, and kinematic response of fish. We propose that the highest priority is to characterize the kinematic response of fish to different turbulent environments such as high shear/turbulence and hydrodynamic disturbances created by solid structures such as deflector and turbine runner blade; the next priority is to map the boundary layer over swimming fish; the last is to document the behavior of freely swimming fish, focusing on fish of our interest. Grid turbulence and Karman vortex street will be employed to map the boundary layers over fish and investigate the effects of environmental disturbances on the swimming performance of fish, because they are well established and documented in engineering literature and are representative of fish's swimming environments. Extreme conditions characteristic of turbine environments, such as strong shear environment and collision, will be investigated. Through controlled laboratory studies, the fish injury mechanism from different sources will be evaluated in isolation. The major goals are to: gain first-hand knowledge of the biological effects under such extreme hydraulic environments in which fish could lack the capability to overcome the perturbations and be vulnerable to injury; Better understand field results by integrating the laboratory studies with the responses of sensor fish device; More importantly, provide well-defined validation cases and boundary conditions for geometry-based computational fluid-structure interaction modeling in order to simulate the complex hydraulic environments in advanced hydropower systems and their effects on fish, greatly enhancing the potential to use CFD as a bio-hydraulic design alternative.« less

New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

PubMed Central

Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

2013-01-01

In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

Fish intake and risk of heart failure: A meta-analysis of five prospective cohort studies

PubMed Central

HOU, LI-NA; LI, FEI; ZHOU, YOU; NIE, SHI-HUAI; SU, LIANG; CHEN, PING-AN; TAN, WAN-LONG; XU, DING-LI

2012-01-01

The findings on the association between fish intake and the risk of heart failure (HF) have been inconsistent. The purpose of this study was to clarify this potential association. We searched for relevant studies in the PubMed database through January 2012 and manually reviewed references. Five independent prospective cohort studies involving 5,273 cases and 144,917 participants were included. The summary relative risk estimates (SRRE) based on the highest compared with the lowest category of fish consumption were estimated by variance-based meta-analysis. In addition, we performed sensitivity and dose-response analyses to examine the association. Overall, an absence of an association between fish intake and HF was observed (SRRE=1.00; 95% CI, 0.81–1.24). However, fried fish intake positively associated with HF (SRRE=1.40; 95% CI, 1.22–1.61). In addition, dose-response analysis of fried fish suggested that each increment of six fried fish per month corresponded to a 37% increase of HF rate (RR=1.37; 95% CI, 1.20–1.56). In conclusion, our findings suggest that there is no significant association between fish intake and risk of HF, with the exception of a possible positive correlation with individuals comsuming fried fish, based on a limited number of studies. Future studies are required to confirm these findings. PMID:23181122

Fish Consumption and Age-Related Macular Degeneration Incidence: A Meta-Analysis and Systematic Review of Prospective Cohort Studies.

PubMed

Zhu, Wei; Wu, Yan; Meng, Yi-Fang; Xing, Qian; Tao, Jian-Jun; Lu, Jiong

2016-11-22

The association between fish consumption and risk of age-related macular degeneration (AMD) is still unclear. The aim of the current meta-analysis and systematic review was to quantitatively evaluate findings from observational studies on fish consumption and the risk of AMD. Relevant studies were identified by searching electronic databases (Medline and EMBASE) and reviewing the reference lists of relevant articles up to August, 2016. Prospective cohort studies that reported relative risks (RRs) and 95% confidence intervals (CIs) for the link between fish consumption and risk of AMD were included. A total of 4202 cases with 128,988 individuals from eight cohort studies were identified in the current meta-analysis. The meta-analyzed RR was 0.76 (95% CI, 0.65-0.90) when any AMD was considered. Subgroup analyses by AMD stages showed that fish consumption would reduce the risk of both early (RR, 0.83; 95% CI, 0.72-0.96) and late (RR; 0.76; 95% CI, 0.60-0.97) AMD. When stratified by the follow-up duration, fish consumption was a protective factor of AMD in both over 10 years ( n = 5; RR, 0.81; 95% CI, 0.67-0.97) and less than 10 years ( n = 3; RR, 0.70; 95% CI, 0.51 to 0.97) follow-up duration. Stratified analyses by fish type demonstrated that dark meat fish (RR, 0.68, 95% CI, 0.46-0.99), especially tuna fish (RR, 0.58; 95% CI, 95% CI, 0.47-0.71) intake was associated with reduced AMD risk. Evidence of a linear association between dose of fish consumption and risk of AMD was demonstrated. The results of this meta-analysis demonstrated that fish consumption can reduce AMD risk. Advanced, well-designed, randomized clinical trials are required in order to validate the conclusions in this study.

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

PubMed Central

Wang, Dan Ohtan; Matsuno, Hitomi; Ikeda, Shuji; Nakamura, Akiko; Yanagisawa, Hiroyuki; Hayashi, Yasunori; Okamoto, Akimitsu

2012-01-01

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO–FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO–FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO–FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO–FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution. PMID:22101241

Synchronization and collective swimming patterns in fish (Hemigrammus bleheri).

PubMed

Ashraf, I; Godoy-Diana, R; Halloy, J; Collignon, B; Thiria, B

2016-10-01

In this work, we address the case of red nose tetra fish Hemigrammus bleheri swimming in groups in a uniform flow, giving special attention to the basic interactions and cooperative swimming of a single pair of fish. We first bring evidence of synchronization of the two fish, where the swimming modes are dominated by 'out-phase' and 'in-phase' configurations. We show that the transition to this synchronization state is correlated with the swimming speed (i.e. the flow rate), and thus with the magnitude of the hydrodynamic pressure generated by the fish body during each swimming cycle. From a careful spatio-temporal analysis corresponding to those synchronized modes, we characterize the distances between the two individuals in a pair in the basic schooling pattern. We test the conclusions of the analysis of fish pairs with a second set of experiments using groups of three fish. By identifying the typical spatial configurations, we explain how the nearest neighbour interactions constitute the building blocks of collective fish swimming. © 2016 The Author(s).

Synchronization and collective swimming patterns in fish (Hemigrammus bleheri)

PubMed Central

Ashraf, I.; Collignon, B.

2016-01-01

In this work, we address the case of red nose tetra fish Hemigrammus bleheri swimming in groups in a uniform flow, giving special attention to the basic interactions and cooperative swimming of a single pair of fish. We first bring evidence of synchronization of the two fish, where the swimming modes are dominated by ‘out-phase’ and ‘in-phase’ configurations. We show that the transition to this synchronization state is correlated with the swimming speed (i.e. the flow rate), and thus with the magnitude of the hydrodynamic pressure generated by the fish body during each swimming cycle. From a careful spatio-temporal analysis corresponding to those synchronized modes, we characterize the distances between the two individuals in a pair in the basic schooling pattern. We test the conclusions of the analysis of fish pairs with a second set of experiments using groups of three fish. By identifying the typical spatial configurations, we explain how the nearest neighbour interactions constitute the building blocks of collective fish swimming. PMID:27798281

CubeSat Nighttime Earth Observations

NASA Astrophysics Data System (ADS)

Pack, D. W.; Hardy, B. S.; Longcore, T.

2017-12-01

Satellite monitoring of visible emissions at night has been established as a useful capability for environmental monitoring and mapping the global human footprint. Pioneering work using Defense Meteorological Support Program (DMSP) sensors has been followed by new work using the more capable Visible Infrared Imaging Radiometer Suite (VIIRS). Beginning in 2014, we have been investigating the ability of small visible light cameras on CubeSats to contribute to nighttime Earth science studies via point-and-stare imaging. This paper summarizes our recent research using a common suite of simple visible cameras on several AeroCube satellites to carry out nighttime observations of urban areas and natural gas flares, nighttime weather (including lighting), and fishing fleet lights. Example results include: urban image examples, the utility of color imagery, urban lighting change detection, and multi-frame sequences imaging nighttime weather and large ocean areas with extensive fishing vessel lights. Our results show the potential for CubeSat sensors to improve monitoring of urban growth, light pollution, energy usage, the urban-wildland interface, the improvement of electrical power grids in developing countries, light-induced fisheries, and oil industry flare activity. In addition to orbital results, the nighttime imaging capabilities of new CubeSat sensors scheduled for launch in October 2017 are discussed.

Signal Cloaking by Electric Fish

PubMed Central

STODDARD, PHILIP K.; MARKHAM, MICHAEL R.

2010-01-01

Electric fish produce weak electric fields to image their world in darkness and to communicate with potential mates and rivals. Eavesdropping by electroreceptive predators exerts selective pressure on electric fish to shift their signals into less-detectable high-frequency spectral ranges. Hypopomid electric fish evolved a signal-cloaking strategy that reduces their detectability by predators in the lab (and thus presumably their risk of predation in the field). These fish produce broad-frequency electric fields close to the body, but the heterogeneous local fields merge over space to cancel the low-frequency spectrum at a distance. Mature males dynamically regulate this cloaking mechanism to enhance or suppress low-frequency energy. The mechanism underlying electric-field cloaking involves electrogenic cells that produce two independent action potentials. In a unique twist, these cells orient sodium and potassium currents in the same direction, potentially boosting their capabilities for current generation. Exploration of such evolutionary inventions could aid the design of biogenerators to power implantable medical devices, an ambition that would benefit from the complete genome sequence of a gymnotiform fish. PMID:20209064

Breast Cancer Diagnostics Based on Spatial Genome Organization

DTIC Science & Technology

2012-07-01

using an already established imaging tool, called NMFA-FLO (Nuclei Manual and FISH automatic). In order to achieve accurate segmentation of nuclei...in tissue we used an artificial neuronal network (ANN)-based supervised pattern recognition approach to screen out well segmented nuclei, after image ... segmentation used to process images for automated nuclear segmentation . Part a) has been adapted from [15] and b) from [16]. Figure 4. Comparison of

Automation of ALK gene rearrangement testing with fluorescence in situ hybridization (FISH): a feasibility study.

PubMed

Zwaenepoel, Karen; Merkle, Dennis; Cabillic, Florian; Berg, Erica; Belaud-Rotureau, Marc-Antoine; Grazioli, Vittorio; Herelle, Olga; Hummel, Michael; Le Calve, Michele; Lenze, Dido; Mende, Stefanie; Pauwels, Patrick; Quilichini, Benoit; Repetti, Elena

2015-02-01

In the past several years we have observed a significant increase in our understanding of molecular mechanisms that drive lung cancer. Specifically in the non-small cell lung cancer sub-types, ALK gene rearrangements represent a sub-group of tumors that are targetable by the tyrosine kinase inhibitor Crizotinib, resulting in significant reductions in tumor burden. Phase II and III clinical trials were performed using an ALK break-apart FISH probe kit, making FISH the gold standard for identifying ALK rearrangements in patients. FISH is often considered a labor and cost intensive molecular technique, and in this study we aimed to demonstrate feasibility for automation of ALK FISH testing, to improve laboratory workflow and ease of testing. This involved automation of the pre-treatment steps of the ALK assay using various protocols on the VP 2000 instrument, and facilitating automated scanning of the fluorescent FISH specimens for simplified enumeration on various backend scanning and analysis systems. The results indicated that ALK FISH can be automated. Significantly, both the Ikoniscope and BioView system of automated FISH scanning and analysis systems provided a robust analysis algorithm to define ALK rearrangements. In addition, the BioView system facilitated consultation of difficult cases via the internet. Copyright © 2015 Elsevier Inc. All rights reserved.

Application of truss analysis for the quantification of changes in fish condition

USGS Publications Warehouse

Fitzgerald, Dean G.; Nanson, Jeffrey W.; Todd, Thomas N.; Davis, Bruce M.

2002-01-01

Conservation of skeletal structure and unique body ratios in fishes facilitated the development of truss analysis as a taxonomic tool to separate physically-similar species. The methodology is predicated on the measurement of across-body distances from a sequential series of connected polygons. Changes in body shape or condition among members of the same species can be quantified with the same technique, and we conducted a feeding experiment using yellow perch (Perca flavescens) to examine the utility of this approach. Ration size was used as a surrogate for fish condition, with fish receiving either a high (3.0% body wt/d) or a low ration (0.5%). Sequentially over our 11-week experiment, replicate ration groups of fish were removed and photographed while control fish were repeatedly weighed and measured. Standard indices of condition (total lipids, weight-length ratios, Fulton's condition) were compared to truss measurements determined from digitized pictures of fish. Condition indices showed similarity between rations while truss measures from the caudal region were important for quantifying changing body shape. These findings identify truss analysis as having use beyond traditional applications. It can potentially be used as a cheap, accurate, and precise descriptor of fish condition in the lab as shown here, and we hypothesize that it would be applicable in field studies.

Comparison of two viewing methods for estimating largemouth bass and walleye ages from sectioned otoliths and dorsal spines

USGS Publications Warehouse

Wegleitner, Eric J.; Isermann, Daniel A.

2017-01-01

Many biologists use digital images for estimating ages of fish, but the use of images could lead to differences in age estimates and precision because image capture can produce changes in light and clarity compared to directly viewing structures through a microscope. We used sectioned sagittal otoliths from 132 Largemouth Bass Micropterus salmoides and sectioned dorsal spines and otoliths from 157 Walleyes Sander vitreus to determine whether age estimates and among‐reader precision were similar when annuli were enumerated directly through a microscope or from digital images. Agreement of ages between viewing methods for three readers were highest for Largemouth Bass otoliths (75–89% among readers), followed by Walleye otoliths (63–70%) and Walleye dorsal spines (47–64%). Most discrepancies (72–96%) were ±1 year, and differences were more prevalent for age‐5 and older fish. With few exceptions, mean ages estimated from digital images were similar to ages estimated via directly viewing the structures through the microscope, and among‐reader precision did not vary between viewing methods for each structure. However, the number of disagreements we observed suggests that biologists should assess potential differences in age structure that could arise if images of calcified structures are used in the age estimation process.

Numerical prediction of the energy efficiency of the three-dimensional fish school using the discretized Adomian decomposition method

NASA Astrophysics Data System (ADS)

Lin, Yinwei

2018-06-01

A three-dimensional modeling of fish school performed by a modified Adomian decomposition method (ADM) discretized by the finite difference method is proposed. To our knowledge, few studies of the fish school are documented due to expensive cost of numerical computing and tedious three-dimensional data analysis. Here, we propose a simple model replied on the Adomian decomposition method to estimate the efficiency of energy saving of the flow motion of the fish school. First, the analytic solutions of Navier-Stokes equations are used for numerical validation. The influences of the distance between the side-by-side two fishes are studied on the energy efficiency of the fish school. In addition, the complete error analysis for this method is presented.

Image analysis for estimating the weight of live animals

NASA Astrophysics Data System (ADS)

Schofield, C. P.; Marchant, John A.

1991-02-01

Many components of animal production have been automated. For example weighing feeding identification and yield recording on cattle pigs poultry and fish. However some of these tasks still require a considerable degree of human input and more effective automation could lead to better husbandry. For example if the weight of pigs could be monitored more often without increasing labour input then this information could be used to measure growth rates and control fat level allowing accurate prediction of market dates and optimum carcass quality to be achieved with improved welfare at minimum cost. Some aspects of animal production have defied automation. For example attending to the well being of housed animals is the preserve of the expert stockman. He gathers visual data about the animals in his charge (in more plain words goes and looks at their condition and behaviour) and processes this data to draw conclusions and take actions. Automatically collecting data on well being implies that the animals are not disturbed from their normal environment otherwise false conclusions will be drawn. Computer image analysis could provide the data required without the need to disturb the animals. This paper describes new work at the Institute of Engineering Research which uses image analysis to estimate the weight of pigs as a starting point for the wider range of applications which have been identified. In particular a technique has been developed to

Detection and genetic analysis of aquabirnaviruses in subclinically infected aquarium fish.

PubMed

Shin, Sang Phil; Gomez, Dennis Kaw; Kim, Ji Hyung; Choresca, Casiano Hermorpia; Han, Jee Eun; Jun, Jin Woo; Park, Se Chang

2011-03-01

Aquabirnaviruses (ABVs) cause serious diseases in a variety of fish species used worldwide in aquaculture and have been isolated from a variety of healthy fish and shellfish species. The type species of ABV is Infectious pancreatic necrosis virus (IPNV), which is the causative agent of a highly contagious disease in juvenile salmonid fish. Marine birnaviruses (MABVs) have been isolated from various marine fish and shellfish. In Korea, ABV infection has been identified in several fish and shellfish. The current study presents sequence data from nested polymerase chain reaction products of 3 ABV strains obtained from different species of asymptomatic aquarium fish collected from a private commercial aquarium in Korea. Phylogenetic analysis of these strains, based on the partial nucleotide sequence of the VP2/NS junction, placed them within the genogroup VII (95-99% bootstrap confidence), which also contains MABV. The subclinically infected fish may be a source of MABV infection for other susceptible fish species inside the aquarium and potentially represent a serious challenge for the management of MABV infections. Additionally, the presence of MABV in these subclinically infected aquarium fish imported from other countries indicates that there is a need for the establishment of appropriate quarantine practices.

Risks and benefits of fish consumption for childbearing women.

PubMed

Del Gobbo, Liana C; Archbold, Josephine A; Vanderlinden, Loren D; Eckley, Chris S; Diamond, Miriam L; Robson, Matthew

2010-01-01

Pregnant women's fish consumption provides both benefits and risks to the developing fetus. Docosahexaenoic acid (DHA) from fish may enhance fetal neurodevelopment, while methylmercury (MeHg) can have detrimental effects. Dietitians would benefit from information on the frequency with which fish species may be consumed to increase DHA intake among Canadian women of childbearing age, and on minimizing the risks from MeHg, especially for those who consume fish frequently. Eighteen fish species were selected for DHA and mercury analysis from retail markets in the Toronto area. Consumption scenarios using analytical results for these fish species indicate that women of childbearing age can consume nine of 18 fish species every day (14 servings a week) or often (up to four servings a week) and remain below toxicological benchmarks for mercury. Moreover, women can also attain the recommended DHA level by consuming six of those nine fish: four 75-g servings of smelt, porgie, or bluefish a week, or two 75-g servings of milkfish, silver pomfret, or tilapia a day. Our analysis indicates that the DHA level recommended for childbearing women can be attained through fish consumption alone, without the need for supplementation and without posing a risk to the woman (or the fetus) from mercury.

Analysis and Evaluation of Parameters Determining Maximum Efficiency of Fish Protection

NASA Astrophysics Data System (ADS)

Khetsuriani, E. D.; Kostyukov, V. P.; Khetsuriani, T. E.

2017-11-01

The article is concerned with experimental research findings. The efficiency of fish fry protection from entering water inlets is the main criterion of any fish protection facility or device. The research was aimed to determine an adequate mathematical model E = f(PCT, Vp, α), where PCT, Vp and α are controlled factors influencing the process of fish fry protection. The result of the processing of experimental data was an adequate regression model. We determined the maximum of fish protection Emax=94,21 and the minimum of optimization function Emin=44,41. As a result of the statistical processing of experimental data we obtained adequate dependences for determining an optimal rotational speed of tip and fish protection efficiency. The analysis of fish protection efficiency dependence E% = f(PCT, Vp, α) allowed the authors to recommend the following optimized operating modes for it: the maximum fish protection efficiency is achieved at the process pressure PCT=3 atm, stream velocity Vp=0,42 m/s and nozzle inclination angle α=47°49’. The stream velocity Vp has the most critical influence on fish protection efficiency. The maximum efficiency of fish protection is obtained at the tip rotational speed of 70.92 rpm.

Comparison of an enzyme-linked immunosorbent assay (ELISA) to gas chromatography (GC) - measurement of polychlorinated biphenyls (PCBs) in selected US fish extracts

USGS Publications Warehouse

Zajicek, J.L.; Tillitt, D.E.; Schwartz, T.R.; Schmitt, C.J.; Harrison, R.O.

2000-01-01

The analysis of PCBs in fish tissues by immunoassay methods was evaluated using fish collected from a US monitoring program, the National Contaminant Biomonitoring Program of the US Department of Interior, Fish and Wildlife Service. Selected composite whole fish samples, which represented widely varying concentrations and sources of PCBs, were extracted and subjected to congener PCB analysis by gas chromatography (GC) and total PCB analysis using an ELISA (ePCBs) calibrated against technical Aroclor 1248. PCB congener patterns in these fishes were different from the patterns found in commercial Aroclors or their combinations as demonstrated by principal component analysis of normalized GC congener data. The sum of the PCB congeners measured by GC (total-PCBs) ranged from 37 to 4600 ng/g (wet weight). Concentrations of PCBs as determined by the ELISA method were positively correlated with total-PCBs and the ePCBs/total-PCBs ratios for individual samples ranged from 1 to 6. Ratios of ePCBs/total-PCBs for dilutions of Aroclors 1242, 1254, and 1260 and for matrix spikes range from 0.6 for 1242 to 2.5 for 1254 and 1260. These results suggest that higher chlorinated PCB congeners have higher affinity for the anti-PCB antibodies. Partial least squares with latent variable analysis of GC and ELISA data of selected Aroclors and fish samples also support the conclusion that ELISA derived PCB concentrations are dependent on the degree on chlorination.

Cavisoma magnum (Cavisomidae), a unique Pacific acanthocephalan redescribed from an unusual host, Mugil cephalus (Mugilidae), in the Arabian Gulf, with notes on histopathology and metal analysis.

PubMed

Amin, Omar M; Heckmann, Richard A; Bannai, Majid A

2018-01-01

Cavisoma magnum (Southwell, 1927) Van Cleave, 1931 was originally described from a sea bass, Serranus sp. and spotted surgeonfish, Ctenochaetus strigosus (Perciformes) off Sri Lanka before its more recent redescription from milkfish in the Philippines in 1995. These reports were based on only light infections of their host fishes. Of the few flathead grey mullets, Mugil cephalus (Mugilidae), that we examined in the Arabian Gulf, one fish was infected with 1,450 worms. One milkfish, Chanos chanos (Chanidae), from the same location in the Arabian Gulf, was also heavily infected with specimens of C. magnum. The descriptions of this unique large worm are revised and for the first time, we provide SEM images, new systematic observations, metal analysis of hooks showing extremely high levels of sulfur, and histopathology in the mullet intestinal tissue. Adjustments and corrections of previous descriptive accounts are made. The histopathology studies show extensive damage to the host intestinal tissue including epithelial necrosis, hemorrhaging and worm encapsulation. There is an extensive amount of host connective tissue surrounding the worm. Results of x-ray analysis displayed high levels of sulfur in proboscis hooks, especially at the tips and edges of these attachment structures. © O.M. Amin et al., published by EDP Sciences, 2018.

Semi-automatic surface sediment sampling system - A prototype to be implemented in bivalve fishing surveys

NASA Astrophysics Data System (ADS)

Rufino, Marta M.; Baptista, Paulo; Pereira, Fábio; Gaspar, Miguel B.

2018-01-01

In the current work we propose a new method to sample surface sediment during bivalve fishing surveys. Fishing institutes all around the word carry out regular surveys with the aim of monitoring the stocks of commercial species. These surveys comprise often more than one hundred of sampling stations and cover large geographical areas. Although superficial sediment grain sizes are among the main drivers of benthic communities and provide crucial information for studies on coastal dynamics, overall there is a strong lack of this type of data, possibly, because traditional surface sediment sampling methods use grabs, that require considerable time and effort to be carried out on regular basis or on large areas. In face of these aspects, we developed an easy and un-expensive method to sample superficial sediments, during bivalve fisheries monitoring surveys, without increasing survey time or human resources. The method was successfully evaluated and validated during a typical bivalve survey carried out on the Northwest coast of Portugal, confirming that it had any interference with the survey objectives. Furthermore, the method was validated by collecting samples using a traditional Van Veen grabs (traditional method), which showed a similar grain size composition to the ones collected by the new method, on the same localities. We recommend that the procedure is implemented on regular bivalve fishing surveys, together with an image analysis system to analyse the collected samples. The new method will provide substantial quantity of data on surface sediment in coastal areas, using a non-expensive and efficient manner, with a high potential application in different fields of research.

Identification of a low digestibility δ-Conglutin in yellow lupin (Lupinus luteus L.) seed meal for atlantic salmon (Salmo salar L.) by coupling 2D-PAGE and mass spectrometry.

PubMed

Ogura, Takahiro; Hernández, Adrián; Aizawa, Tomoko; Ogihara, Jun; Sunairi, Michio; Alcaino, Javier; Salvo-Garrido, Haroldo; Maureira-Butler, Iván J

2013-01-01

The need of quality protein in the aquaculture sector has forced the incorporation of alternative plant proteins into feeding diets. However, most plant proteins show lower digestibility levels than fish meal proteins, especially in carnivorous fishes. Manipulation of protein content by plant breeding can improve the digestibility rate of plant proteins in fish, but the identification of low digestibility proteins is essential. A reduction of low digestibility proteins will not only increase feed efficiency, but also reduce water pollution. Little is known about specific digestible protein profiles and/or molecular identification of more bioavailable plant proteins in fish diets. In this study, we identified low digestibility L. luteus seed proteins using Atlantic salmon (Salmo salar) crude digestive enzymes in an in vitro assay. Low digestibility proteins were identified by comparing SDS-PAGE banding profiles of digested and non-digested lupin seed proteins. Gel image analysis detected a major 12 kDa protein band in both lupin meal and protein isolate digested products. The 12 kDa was confirmed by 2D-PAGE gels and the extracted protein was analyzed with an ion trap mass spectrometer in tandem mass mode. The MS/MS data showed that the 12 kDa low digestibility protein was a large chain δconglutin, a common seed storage protein of yellow lupin. Comparison of the protein band profiles between lupin meal and protein isolates showed that the isolatation process did not affect the low digestibility of the 12 kDa protein.

Identification of a Low Digestibility δ-Conglutin in Yellow Lupin (Lupinus luteus L.) Seed Meal for Atlantic Salmon (Salmo salar L.) by Coupling 2D-PAGE and Mass Spectrometry

PubMed Central

Ogura, Takahiro; Hernández, Adrián; Aizawa, Tomoko; Ogihara, Jun; Sunairi, Michio; Alcaino, Javier; Salvo-Garrido, Haroldo; Maureira-Butler, Iván J.

2013-01-01

The need of quality protein in the aquaculture sector has forced the incorporation of alternative plant proteins into feeding diets. However, most plant proteins show lower digestibility levels than fish meal proteins, especially in carnivorous fishes. Manipulation of protein content by plant breeding can improve the digestibility rate of plant proteins in fish, but the identification of low digestibility proteins is essential. A reduction of low digestibility proteins will not only increase feed efficiency, but also reduce water pollution. Little is known about specific digestible protein profiles and/or molecular identification of more bioavailable plant proteins in fish diets. In this study, we identified low digestibility L. luteus seed proteins using Atlantic salmon (Salmo salar) crude digestive enzymes in an in vitro assay. Low digestibility proteins were identified by comparing SDS-PAGE banding profiles of digested and non-digested lupin seed proteins. Gel image analysis detected a major 12 kDa protein band in both lupin meal and protein isolate digested products. The 12 kDa was confirmed by 2D-PAGE gels and the extracted protein was analyzed with an ion trap mass spectrometer in tandem mass mode. The MS/MS data showed that the 12 kDa low digestibility protein was a large chain δconglutin, a common seed storage protein of yellow lupin. Comparison of the protein band profiles between lupin meal and protein isolates showed that the isolatation process did not affect the low digestibility of the 12 kDa protein. PMID:24278278

An algorithm to track laboratory zebrafish shoals.

PubMed

Feijó, Gregory de Oliveira; Sangalli, Vicenzo Abichequer; da Silva, Isaac Newton Lima; Pinho, Márcio Sarroglia

2018-05-01

In this paper, a semi-automatic multi-object tracking method to track a group of unmarked zebrafish is proposed. This method can handle partial occlusion cases, maintaining the correct identity of each individual. For every object, we extracted a set of geometric features to be used in the two main stages of the algorithm. The first stage selected the best candidate, based both on the blobs identified in the image and the estimate generated by a Kalman Filter instance. In the second stage, if the same candidate-blob is selected by two or more instances, a blob-partitioning algorithm takes place in order to split this blob and reestablish the instances' identities. If the algorithm cannot determine the identity of a blob, a manual intervention is required. This procedure was compared against a manual labeled ground truth on four video sequences with different numbers of fish and spatial resolution. The performance of the proposed method is then compared against two well-known zebrafish tracking methods found in the literature: one that treats occlusion scenarios and one that only track fish that are not in occlusion. Based on the data set used, the proposed method outperforms the first method in correctly separating fish in occlusion, increasing its efficiency by at least 8.15% of the cases. As for the second, the proposed method's overall performance outperformed the second in some of the tested videos, especially those with lower image quality, because the second method requires high-spatial resolution images, which is not a requirement for the proposed method. Yet, the proposed method was able to separate fish involved in occlusion and correctly assign its identity in up to 87.85% of the cases, without accounting for user intervention. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effectiveness of Quantitative Real Time PCR in Long-Term Follow-up of Chronic Myeloid Leukemia Patients.

PubMed

Savasoglu, Kaan; Payzin, Kadriye Bahriye; Ozdemirkiran, Fusun; Berber, Belgin

2015-08-01

To determine the use of the Quantitative Real Time PCR (RQ-PCR) assay follow-up with Chronic Myeloid Leukemia (CML) patients. Cross-sectional observational. Izmir Ataturk Education and Research Hospital, Izmir, Turkey, from 2009 to 2013. Cytogenetic, FISH, RQ-PCR test results from 177 CMLpatients' materials selected between 2009 - 2013 years was set up for comparison analysis. Statistical analysis was performed to compare between FISH, karyotype and RQ-PCR results of the patients. Karyotyping and FISH specificity and sensitivity rates determined by ROC analysis compared with RQ-PCR results. Chi-square test was used to compare test failure rates. Sensitivity and specificity values were determined for karyotyping 17.6 - 98% (p=0.118, p > 0.05) and for FISH 22.5 - 96% (p=0.064, p > 0.05) respectively. FISH sensitivity was slightly higher than karyotyping but there was calculated a strong correlation between them (p < 0.001). RQ-PCR test failure rate did not correlate with other two tests (p > 0.05); however, karyotyping and FISH test failure rate was statistically significant (p < 0.001). Besides, the situation needed for karyotype analysis, RQ-PCR assay can be used alone in the follow-up of CMLdisease.

Utilization of fish bone as adsorbent of Fe3+ ion by controllable removal of its carbonaceous component

NASA Astrophysics Data System (ADS)

Nurhadi, M.; Kusumawardani, R.; Widiyowati, I. I.; Wirhanuddin; Nur, H.

2018-05-01

The performance of fish bone to adsorb Fe3+ ion in solution was studied. Powdered fish bone and carbonized fish bone were used as adsorbent. All absorbents were characterized by X-ray diffraction (XRD), IR spectroscopy, nitrogen adsorption, scanning electron microscopy (SEM) and TG analysis. Powdered fish bone and carbonized fish bone were effective as adsorbent for removing Fe3+ ion in solution. The metal adsorptions of Fe3+ ion were 94 and 98% for powdered fish bone and fish bone which carbonized at 400 and 500 °C.

Evaluation of the damage in fish spermatozoa cryopreservation

NASA Astrophysics Data System (ADS)

Li, Jun; Liu, Qinghua; Zhang, Shicui

2006-12-01

Cryodamages occur during sperm cryopreservation. Cryopreservation of fish sperm usually results in marked decrease in sperm quality, such as swelling or disruption of the plasma membrane, mitochondrial dysfunction, diminished sperm motility, impaired velocity, shorter motility period, denaturation, and release of some enzymes from spermatozoa. In this paper, damages in morphology, physiology, biochemistry and metabolism, and genetic integrity of fish semen after cryopreservation are discussed. New approaches in assessment of fish thawed sperm quality such as computer assisted sperm analysis, flow cytometic analysis combined with fluorescent probes and single cell gel electrophoresis are also briefly reviewed.

Nanoparticle mucoadhesive system as a new tool for fish immune system modulation.

PubMed

Charlie-Silva, Ives; de Melo, Nathalie Ferreira Silva; Gomes, Juliana M M; Fraceto, Leonardo Fernandes; de Melo, Daniela Chemim; de Oliveira Silva, Juliana; de Barros, André Luis Branco; Corrêa Junior, Jose Dias

2018-05-30

Recently, chitosan-based nanoparticles with mucoadhesive properties emerged as a strategy for mucosal drug release. This study aimed to characterize the interaction of mucoadhesive system chitosancoated PLGA nanoparticles (NPMA) with fish external mucus. NP suspensions with fluorescent probe were prepared and characterized by size, polydispersity, zeta potential and pH measures. In post-exposure fish were observed an increase in fluorescence imaging over time and it was significantly influenced by NPMA concentration. We also observed the main predominance the fluorescence in the spleen, followed by liver, gill and other tissues. The use of mucoadhesive nanocarriers becomes an alternative for administration of drugs and immunomodulators in immersion systems since the nanosystem can adhere to the mucosal surface of the fish with little residual effect in the water. Copyright © 2018. Published by Elsevier Ltd.

Unsteady Flow Interactions Between Pitching Wings In Schooling Arrangements

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2017-11-01

In nature, many fish aggregate into large groups or schools for protection against predators, for social interactions and to save energy during migrations. Regardless of their prime motivation, fish experience three-dimensional flow interactions amongst themselves that can improve or hamper swimming performance and give rise to fluid-mediated forces between individuals. To date, the unsteady, three-dimensional flow interactions among schooling fish remains relatively unexplored. In order to study these interactions, the caudal fins of two interacting fish are idealized as two finite span pitching wings arranged in mixtures of canonical in-line and side-by-side arrangements. The forces and moments acting on the wings in the streamwise and cross-stream directions are quantified as the arrangement and the phase delay between the wings is altered. Particle image velocimetry is employed to characterize the flow physics during high efficiency locomotion. Finally, the forces and flowfields of two-dimensional pitching wings are compared with three-dimensional wings to distinguish how three-dimensionality alters the flow interactions in schools of fish.

Biogenic Fish-gut Calcium Carbonate is a Stable Amorphous Phase in the Gilt-head Seabream, Sparus aurata

PubMed Central

Foran, Elizabeth; Weiner, Steve; Fine, Maoz

2013-01-01

The main source of calcium carbonate (CaCO3) in the ocean comes from the shells of calcifying planktonic organisms, but substantial amounts of CaCO3 are also produced in fish intestines. The precipitation of CaCO3 assists fish in intestinal water absorption and aids in whole body Ca2+ homeostasis. Here we report that the product formed in the intestinal lumen of the gilt-head seabream, Sparus aurata, is an amorphous calcium carbonate (ACC) phase. With FTIR spectroscopy and SEM imaging, our study shows that the fish-derived carbonates from S. aurata are maintained as a stable amorphous phase throughout the intestinal tract. Moreover, intestinal deposits contained up to 54 mol% Mg2+, the highest concentration yet reported in biogenic ACC. Mg is most likely responsible for stabilizing this inherently unstable mineral. The fish carbonates also displayed initial rapid dissolution when exposed to seawater, exhibiting a significant increase in carbonate concentration. PMID:23609008

Relationships between mercury concentration and food selectivity of many kinds of fishes in Minamata Bay

NASA Astrophysics Data System (ADS)

Mori, K.; Kanaya, G.

2016-02-01

Serious injuries occurred in residents who consumed fish and shellfishes in Minamata Bay polluted by high-concentration methyl-mercury in the 1950s. Pollution has fallen to a safe level because of the pollution prevention project (dredging etc.) carried out from 1977 to 1990. From 2010 we have been researching the bioaccumulation of mercury in several fishes in Minamata Bay and surrounding areas. We selected several sampling points that showed different environmental conditions, species composition and food web patterns. For the determination of feeding types of 60 species fishes (600 samples) sampled by gill net, we measured mercury levels of each sample and directly checked food items in gut, and distinguished carnivore, omnivore, herbivore and detritivore. At this time, we introduced a stable isotope analysis for checking the food history and feeding habits of dominant fish. In about 300 individuals of 30 species of dominant fish selected from the 600 samples, we measured the stable nitrogen and carbon isotope ratios (δ15N, δ13C) of each sample. Checking the food items in gut of fishes, more than 80% of fishes were carnivorous, and showed different selectivity of food items, such as fish, crustacean and so on. From the results of stable isotope ratios, benthic fish tended to show a higher ratio of δ13C. Usually benthic microalgae evidenced a higher ratio of δ13C than planktonic microalgae, and the ratio conservative through the food chain. In general, δ15N increases through the food chain with +3 to +4 ‰ enrichment per trophic step. In these data, carnivorous fishes of benthic and pelagic type showed medium and high ratios of δ15N. From comparing the stable isotope ratio to the mercury concentration of fishes, all of the high-mercury fishes belonged to benthic and carnivorous types. We consider the joint method of food web analysis and stable isotope analysis to be useful for understanding the mechanism of mercury bioaccumulation through the food web

To breathe or fight? Siamese fighting fish differ when facing a real opponent or mirror image.

PubMed

Arnott, Gareth; Beattie, Emma; Elwood, Robert W

2016-08-01

Displays are a feature of animal contest behaviour and have been interpreted as a means of gathering information on opponent fighting ability, as well as signalling aggressive motivation. In fish, contest displays often include frontal and lateral elements, which in the latter involves contestants showing their flanks to an opponent. Previous work in a range of fish species has demonstrated population-level lateralization of these displays, preferentially showing one side to their opponent. Mirrors are commonly used in place of a real opponent to study aggression in fish, yet they may disrupt the normal pattern of display behaviour. Here, using Siamese fighting fish, Betta splendens, we compare the aggressive behaviour of males to a mirror image and real opponent behind a transparent barrier. As this species is a facultative air-breather, we also quantify surface breathing, providing insights into underlying fight motivation. Consistent with previous work, we found evidence of population-level lateralization, with a bias to present the left side and use the left eye when facing a real opponent. Contrary to expectations, there were no differences in the aggressive displays to a mirror and real opponent, with positive correlations between the behaviour in the two scenarios. However, there were important differences in surface breathing, which was more frequent and of longer duration in the mirror treatment. The reasons for these differences are discussed in relation to the repertoire of contest behaviour and motivation when facing a real opponent. Copyright © 2016 Elsevier B.V. All rights reserved.

Sidescan-sonar mapping of benthic trawl marks on the shelf and slope off Eureka, California

USGS Publications Warehouse

Friedlander, A.M.; Boehlert, G.W.; Field, M.E.; Mason, J.E.; Gardner, J.V.; Dartnell, P.

1999-01-01

The abundance and orientation of trawl marks was quantified over an extensive portion (>2700 km2) of the Eureka, California, outer shelf and slope, an important commercial bottom trawling ground for such high-value species as rockfish, sole, and sablefish. Fishing logbook data indicate that the entire reporting area was trawled about one and a half times on an average annual basis and that some areas were trawled over three times annually. High-resolution sidescan-sonar images of the study area revealed deep gouges on the seafloor, caused by heavy steel trawl doors that act to weigh down and spread open the bottom trawls. These trawl marks are commonly oriented parallel to bathymetric contours and many could be traced for several kilometers. Trawl marks showed a quadratic relationship in relation to water depth, with the greatest number of trawl marks observed at ~400 m. There was a significant positive correlation between the number of trawl marks observed on the sidescan images and the number of annual trawl hours logged within reporting areas. This finding indicates that acoustic remote sensing is a promising independent approach to evaluate fishing effort on a scale consistent with commercial fishing activities. Bottom trawling gear is known to modify seafloor habitats by altering benthic habitat complexity and by removing or damaging infauna and sessile organisms. Identifying the extent of trawling in these areas may help determine the effects of this type of fishing gear on the benthos and develop indices of habitat disturbance caused by fishing activities.

Prevalence of cymothoid isopods (Crustacea, Isopoda) and proximate analysis of parasites and their host fishes, Southeastern India.

PubMed

Rajaram, Rajendran; Rakesh Kumar, Kulanthasamy; Vinothkumar, Shanmugam; Metillo, Ephrime B

2018-06-01

Cymothoid isopods (Crustacea, Isopoda) are considered as potential threat to the health of different fish species. In order to evaluate the prevalence and proximate analysis of Cymothoid isopods and its host, an investigation was carried out fish species belonging to families Hemiramphidae and Belonidae in the Palk Bay region, Southeastern India. A total of 1265 individuals of teleost fish belonging to family Hemiramphidae species, Hemiramphus far (462), H. archipelagicus (78), and H. lutkie (277) and another family Belonidae species, Tylosurus crocodilus (448), were examined for cymothoid ectoparasitic infestation. Prevalence in H. far was the highest (39%) for the cymothoid Mothocys plagulophora , while T. crocodilus was most infested (13%) with Mothocys renardi, H. far and H. lutkie were not infested by M. renardi while T. crocodilus was not infested by M. plagulophora. Proximate analysis showed reduced level of protein in parasite infested fish compared with non-infested individuals. However, carbohydrate and lipid concentrations were lower in infested fish than non-infested individuals. Proximate analysis values in the two parasites of Mothocys species were similar, and these values were comparable to those unaffected fish species indicating that parasites were well nourished. The proximate analysis of isopod parasite M. plagulophora showed 21.6 ± 7.7, 1.26 ± 0.05, 5.49 ± 1.06% of protein, carbohydrate and lipid respectively, and in M. renardi, 21.09 ± 6.6, 1.32 ± 0.12, 5.83 ± 0.72% of protein, carbohydrate and lipid respectively. Cadmium levels were similar between affected and non-affected fish individuals and among species. The Pb levels were comparable among all T. crocodilus individuals, but the levels of Cd not showed much variation between affected and unaffected individuals in all four fish species.

Zebrafish Craniofacial Development: A Window into Early Patterning

PubMed Central

Mork, Lindsey; Crump, Gage

2016-01-01

The formation of the face and skull involves a complex series of developmental events mediated by cells derived from the neural crest, endoderm, mesoderm, and ectoderm. Although vertebrates boast an enormous diversity of adult facial morphologies, the fundamental signaling pathways and cellular events that sculpt the nascent craniofacial skeleton in the embryo have proven to be highly conserved from fish to man. The zebrafish Danio rerio, a small freshwater cyprinid fish from eastern India, has served as a popular model of craniofacial development since the 1990s. Unique strengths of the zebrafish model include a simplified skeleton during larval stages, access to rapidly developing embryos for live imaging, and amenability to transgenesis and complex genetics. In this chapter, we describe the anatomy of the zebrafish craniofacial skeleton; its applications as models for the mammalian jaw, middle ear, palate, and cranial sutures; the superior imaging technology available in fish that has provided unprecedented insights into the dynamics of facial morphogenesis; the use of the zebrafish to decipher the genetic underpinnings of craniofacial biology; and finally a glimpse into the most promising future applications of zebrafish craniofacial research. PMID:26589928

Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

PubMed

Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

2014-02-01

While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

A hedonic price analysis of the outfitter market for trout fishing in the Rocky Mountain West

Treesearch

Heidi M. Pitts; Jennifer A. Thacher; Patricia A. Champ; Robert P. Berrens

2012-01-01

Trout is the most popular sport fish in Montana, Wyoming, Colorado, and New Mexico where fishing outfitters bring revenues to many rural economies. This article uses the hedonic pricing method on a monopolistically competitive outfitter market in those four states to examine angler values for trout fishing characteristics. A total of 1,685 fishing trip observations...

A Method for Measuring Fishing Effort by Small-Scale Fish Aggregating Device (FAD) Fishers from the Commonwealth of Dominica

ERIC Educational Resources Information Center

Alvard, Michael; McGaffey, Ethan; Carlson, David

2015-01-01

We used global positioning system (GPS) technology and tracking analysis to measure fishing effort by marine, small-scale, fish aggregating device (FAD) fishers of the Commonwealth of Dominica. FADs are human-made structures designed to float on the surface of the water and attract fish. They are also prone to common pool resource problems. To…

Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

PubMed Central

Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

2008-01-01

Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

Business Profile of Boat Lift Net and Stationary Lift Net Fishing Gear in Morodemak Waters Central Java

NASA Astrophysics Data System (ADS)

Hapsari, Trisnani D.; Jayanto, Bogi B.; Fitri, Aristi D. P.; Triarso, I.

2018-02-01

Lift net is one of the fishing gears that is used widely in the Morodemak coastal fishing port (PPP) for catching pelagic fish. The yield of fish captured by these fishing gear has high economic value, such as fish belt (Trichiurus sp), squids (Loligo sp) and anchovies (Stelophorus sp). The aims of this research were to determine the technical aspects of boat lift net and stationary lift net fishing gear in Morodemak Waters Demak Regency; to find out the financial aspect of those fishing gears and to analyze the financial feasibility by counting PP, NPV, IRR, and B/C ratio criteria. This research used case study method with descriptive analysis. The sampling method was purposive sampling with 22 fishermen as respondents. The result of the research showed that the average of boat lift net acceptance was Rp 388,580,000. The financial analysis of fisheries boat lift net with the result of NPV Rp 836,149,272, PP 2.44 years, IRR value 54%, and B/C ratio 1.73. The average of stationary lift net acceptance was Rp 27,750,000. The financial analysis lift net with the result of NPV Rp 37,937,601; PP 1.96 years, IRR value 86%, and B/C ratio 1.32. This research had a positive NPV value, B/C ratio >1, and IRR > discount rate (12 %). This study concluded that the fishery business of boat lift net and stationary lift net in Morodemak coastal fishing port (PPP) was worth running.

Sediment profile imaging (SPI) and micro-electrode technologies in impact assessment studies: Example from two fjords in Southern Chile used for fish farming

NASA Astrophysics Data System (ADS)

Mulsow, S.; Krieger, Y.; Kennedy, R.

2006-10-01

Two state-of-the-art techniques were used to assess the impact of organic loading from fish farming in two fjords of Southern Chile, Pillan and Reñihue Fjords. A sediment profile imaging (SPI) camera was deployed and sediment microprofiles (oxygen, H 2S, redox and pH) were measured in undisturbed sediment cores collected using a HAPS corer. Four out of seven stations in Pillan Fjord were found to be severely disturbed: SPI images showed azoic conditions (no apparent Redox Potential Discontinuity layer, no evidence of aerobic life form, presence of an uneaten fish food layer, negative OSI scores). These findings were corroborated by very high oxygen consumption rates (700-1200 mmol m - 2 day - 1 ), H 2S concentrations increasing quickly within the sediment column and redox potential decreasing towards negative values within a few mm down core. Results for Reñihue Fjord were not so straightforward. SPI images indicated that most of the stations (R3 to R7) presented well-mixed conditions (high apparent RPD layers, presence of infauna, burrows, etc.), but oxygen profiles yielded consumption rates of 230 to 490 mmol m - 2 day - 1 and organic carbon mineralization of 2.16 to 4.53 g C m - 2 day - 1 . These latter values were close to the limit of aerobic degradation of organic matter although no visible changes were recorded within the sediment column. In view of our findings, the importance of integrating multidisciplinary methodologies in impact assessment studies was discussed.

Parasite infestation increases on coral reefs without cleaner fish

NASA Astrophysics Data System (ADS)

Grutter, A. S.; De Brauwer, M.; Bshary, R.; Cheney, K. L.; Cribb, T. H.; Madin, E. M. P.; McClure, E. C.; Meekan, M. G.; Sun, D.; Warner, R. R.; Werminghausen, J.; Sikkel, P. C.

2018-03-01

Mutualisms are pivotal in shaping ecological communities. Iconic images of cleaner fish entering the mouths of predatory fish clients to remove ectoparasites epitomize their mutual benefit. Experimental manipulations of cleaner wrasse reveal declines in fish size and growth, and population abundance and diversity of client fishes in the absence of cleaner wrasse. Fishes grow more slowly and are less abundant and diverse on reefs without cleaner wrasse, both for larger species that are regularly cleaned and have high ectoparasite loads ("attractive species"), and for those smaller species that are rarely cleaned and are rarely infested with parasites ("unattractive species"). We therefore considered whether these previously observed declines in individual and population parameters on reefs without cleaners were related to increased ectoparasite infestation using an attractive species ( Hemigymnus melapterus, Labridae) and an unattractive species ( Pomacentrus amboinensis, Pomacentridae). Traps with these fish as a form of bait were deployed to sample blood-sucking gnathiid ectoparasites (Gnathiidae: Isopoda) on reefs from which cleaners ( Labroides dimidiatus, Labridae) have been removed for 13 yr. Cleaner fish could not enter traps to access the clients/hosts, but gnathiids could enter the traps to infest hosts; thus, this method sampled the indirect effect of cleaners on gnathiid infestation of fish. Infestation was higher on reefs without cleaners than on those with them. The effect was only detected during the daytime when cleaners are active and only on the attractive species ( H. melapterus). Thus, cleaner presence indirectly reduced fish exposure to parasites in a species that is highly susceptible to parasites, but not in one that is rarely infested with parasites. This suggests that cleaner presence indirectly reduces exposure of a common fish species to harmful parasites, which may explain some observed benefits in fishes at this location.

Evaluation of Fish Passage at Whitewater Parks Using 2D and 3D Hydraulic Modeling

NASA Astrophysics Data System (ADS)

Hardee, T.; Nelson, P. A.; Kondratieff, M.; Bledsoe, B. P.

2016-12-01

In-stream whitewater parks (WWPs) are increasingly popular recreational amenities that typically create waves by constricting flow through a chute to increase velocities and form a hydraulic jump. However, the hydraulic conditions these structures create can limit longitudinal habitat connectivity and potentially inhibit upstream fish migration, especially of native fishes. An improved understanding of the fundamental hydraulic processes and potential environmental effects of whitewater parks is needed to inform management decisions about Recreational In-Channel Diversions (RICDs). Here, we use hydraulic models to compute a continuous and spatially explicit description of velocity and depth along potential fish swimming paths in the flow field, and the ensemble of potential paths are compared to fish swimming performance data to predict fish passage via logistic regression analysis. While 3d models have been shown to accurately predict trout movement through WWP structures, 2d methods can provide a more cost-effective and manager-friendly approach to assessing the effects of similar hydraulic structures on fish passage when 3d analysis in not feasible. Here, we use 2d models to examine the hydraulics in several WWP structures on the North Fork of the St. Vrain River at Lyons, Colorado, and we compare these model results to fish passage predictions from a 3d model. Our analysis establishes a foundation for a practical, transferable and physically-rigorous 2d modeling approach for mechanistically evaluating the effects of hydraulic structures on fish passage.

Total Fat, n-3 Fatty Acids and Vitamin D3 in Selected Fish Species Sampled Under USDA’s National Food and Nutrient Analysis Program (NFNAP)

USDA-ARS?s Scientific Manuscript database

As part of the USDA’s National Food and Nutrient Analysis Program (NFNAP), new analytical data were determined for the 20 most frequently consumed raw fish identified for FDA’s voluntary nutrition labeling. Samples of 21 fish species were purchased from 12 supermarkets nationwide according to a sta...

ALK rearrangement in a large series of consecutive non-small cell lung cancers: comparison between a new immunohistochemical approach and fluorescence in situ hybridization for the screening of patients eligible for crizotinib treatment.

PubMed

Alì, Greta; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Lupi, Cristiana; Sensi, Elisa; Giannini, Riccardo; Borrelli, Nicla; Menghi, Maura; Chella, Antonio; Ribechini, Alessandro; Cappuzzo, Federico; Melfi, Franca; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2014-11-01

Echinoderm microtubule associated proteinlike 4-anaplastic lymphoma receptor tyrosine kinase (EML4-ALK) translocation has been described in a subset of patients with non-small cell lung cancer (NSCLC) and has been shown to have oncogenic activity. Fluorescence in situ hybridization (FISH) is used to detect ALK-positive NSCLC, but it is expensive, time-consuming, and difficult for routine application. To evaluate the potential role of immunohistochemistry (IHC) as a screening tool to identify candidate cases for FISH analysis and for ALK inhibitor therapy in NSCLC. We performed FISH and IHC for ALK and mutational analysis for epidermal growth factor receptor (EGFR) and KRAS in 523 NSCLC specimens. We conducted IHC analysis with the monoclonal antibody D5F3 (Ventana Medical Systems, Tucson, Arizona) and a highly sensitive detection system. We also performed a MassARRAY-based analysis (Sequenom, San Diego, California) in a small subset of 11 samples to detect EML4-ALK rearrangement. Of the 523 NSCLC specimens, 20 (3.8%) were positive for ALK rearrangement by FISH analysis. EGFR and KRAS mutations were identified in 70 (13.4%) and 124 (23.7%) of the 523 tumor samples, respectively. ALK rearrangement and EGFR and KRAS mutations were mutually exclusive. Of 523 tumor samples analyzed, 18 (3.4%) were ALK(+) by IHC, 18 samples (3.4%) had concordant IHC and FISH results, and 2 ALK(+) cases (0.3%) by FISH failed to show ALK protein expression. In the 2 discrepant cases, we did not detect any mass peaks for the EML4-ALK variants by MassARRAY. Our results show that IHC may be a useful technique for selecting NSCLC cases to undergo ALK FISH analysis.

Visual reinforcement in the female Siamese fighting fish, Betta splendens.

PubMed

Elcoro, Mirari; Silva, Stephanie P; Lattal, Kennon A

2008-07-01

Operant conditioning with Betta splendens (Bettas) has been investigated extensively using males of the species. Ethological studies of female Bettas have revealed aggressive interactions that qualitatively parallel those between male Bettas. Given these similarities, four experiments were conducted with female Bettas to examine the generality of a widely reported finding with males: mirror-image reinforcement. Swimming through a ring was reinforced by a 10-s mirror presentation. As with males, ring swimming was acquired and maintained when mirror presentations were immediate (Experiments 1, 2, and 3) and delayed (Experiment 4). The failure of conventional extinction (Experiments 1 and 2) and response-independent mirror presentations (Experiment 3) to maintain responding confirmed the reinforcing properties of mirror presentation. These results extend previous findings of mirror images as reinforcers in males of the same species and illustrate a complementarity between behavioral ecology and the experimental analysis of behavior.

Non-invasive imaging of zebrafish with spinal deformities using optical coherence tomography: a preliminary study

NASA Astrophysics Data System (ADS)

Bernstein, Liane; Beaudette, Kathy; Patten, Kessen; Beaulieu-Ouellet, Émilie; Strupler, Mathias; Moldovan, Florina; Boudoux, Caroline

2013-03-01

A zebrafish model has recently been introduced to study various genetic mutations that could lead to spinal deformities such as scoliosis. However, current imaging techniques make it difficult to perform longitudinal studies of this condition in zebrafish, especially in the early stages of development. The goal of this project is to determine whether optical coherence tomography (OCT) is a viable non-invasive method to image zebrafish exhibiting spinal deformities. Images of both live and fixed malformed zebrafish (5 to 21 days postfertilization) as well as wild-type fish (5 to 29 days postfertilization) were acquired non-invasively using a commercial SD-OCT system, with a laser source centered at 930nm (λ=100nm), permitting axial and lateral resolutions of 7 and 8μm respectively. Using two-dimensional images and three-dimensional reconstructions, it was possible to identify the malformed notochord as well as deformities in other major organs at different stages of formation. Visualization of the notochord was facilitated with the development of a segmentation algorithm. OCT images were compared to HE histological sections and images obtained by calcein staining. Because of the possibility of performing longitudinal studies on a same fish and reducing image processing time as compared with staining techniques and histology, the use of OCT could facilitate phenotypic characterization in studying genetic factors leading to spinal deformities in zebrafish and could eventually contribute to the identification of the genetic causes of spinal deformities such as scoliosis.

Near-Infrared Spectroscopy and Imaging Studies of Fertilized Fish Eggs: In Vivo Monitoring of Egg Growth at the Molecular Level

NASA Astrophysics Data System (ADS)

Ishigaki, Mika; Kawasaki, Shoya; Ishikawa, Daitaro; Ozaki, Yukihiro

2016-01-01

In this work, the growth of fertilized Japanese medaka (Oryzias latipes) eggs was monitored in vivo at the molecular level using near-infrared (NIR) spectroscopy and NIR imaging. NIR spectra were recorded noninvasively for three major parts of a fertilized medaka egg, the embryonic body, the oil droplets, and the yolk, from the first day after fertilization to the day before hatching. Principal component analysis (PCA) revealed that water, protein, and lipid contents in the egg yolk and oil droplets changed significantly just before hatching. The ratio of the characteristic peaks due to proteins and lipids in the second derivative spectra suggested that the relative concentration of proteins to lipids was constant in the egg yolk, while it dramatically increased just before hatching in the oil droplets. Furthermore, linear discriminant analysis (LDA) predicted the hatching possibility on the next day with 100% and 99.3% accuracy for yolk and oil droplets data, respectively. Two types of NIR images were developed in situ using the band intensities of the lipids and proteins in the second derivative spectra. The egg’s protein and lipid content was successfully visualized noninvasively. This technique should enable noninvasive quality testing of fertilized eggs in the future.

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species.

PubMed

Cardinale, Massimiliano; Kaiser, Dominik; Lueders, Tillmann; Schnell, Sylvia; Egert, Markus

2017-07-19

The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454-pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH-CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH-CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm-like structures occurred. Image analysis showed local densities of up to 5.4 * 10 10 cells per cm 3 , and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.

Why fish oil fails: a comprehensive 21st century lipids-based physiologic analysis.

PubMed

Peskin, B S

2014-01-01

The medical community suffered three significant fish oil failures/setbacks in 2013. Claims that fish oil's EPA/DHA would stop the progression of heart disease were crushed when The Risk and Prevention Study Collaborative Group (Italy) released a conclusive negative finding regarding fish oil for those patients with high risk factors but no previous myocardial infarction. Fish oil failed in all measures of CVD prevention-both primary and secondary. Another major 2013 setback occurred when fish oil's DHA was shown to significantly increase prostate cancer in men, in particular, high-grade prostate cancer, in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) analysis by Brasky et al. Another monumental failure occurred in 2013 whereby fish oil's EPA/DHA failed to improve macular degeneration. In 2010, fish oil's EPA/DHA failed to help Alzheimer's victims, even those with low DHA levels. These are by no means isolated failures. The promise of fish oil and its so-called active ingredients EPA / DHA fails time and time again in clinical trials. This lipids-based physiologic review will explain precisely why there should have never been expectation for success. This review will focus on underpublicized lipid science with a focus on physiology.

Why Fish Oil Fails: A Comprehensive 21st Century Lipids-Based Physiologic Analysis

PubMed Central

Peskin, B. S.

2014-01-01

The medical community suffered three significant fish oil failures/setbacks in 2013. Claims that fish oil's EPA/DHA would stop the progression of heart disease were crushed when The Risk and Prevention Study Collaborative Group (Italy) released a conclusive negative finding regarding fish oil for those patients with high risk factors but no previous myocardial infarction. Fish oil failed in all measures of CVD prevention—both primary and secondary. Another major 2013 setback occurred when fish oil's DHA was shown to significantly increase prostate cancer in men, in particular, high-grade prostate cancer, in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) analysis by Brasky et al. Another monumental failure occurred in 2013 whereby fish oil's EPA/DHA failed to improve macular degeneration. In 2010, fish oil's EPA/DHA failed to help Alzheimer's victims, even those with low DHA levels. These are by no means isolated failures. The promise of fish oil and its so-called active ingredients EPA / DHA fails time and time again in clinical trials. This lipids-based physiologic review will explain precisely why there should have never been expectation for success. This review will focus on underpublicized lipid science with a focus on physiology. PMID:24551453

Analyzing the association between fish consumption and osteoporosis in a sample of Chinese men.

PubMed

Li, Xia; Lei, Tao; Tang, Zihui; Dong, Jingcheng

2017-04-19

The main purpose of this study was to estimate the associations between frequency of fish food consumption and osteoporosis (OP) in general Chinese men. We conducted a large-scale, community-based, cross-sectional study to investigate the associations by using self-report questionnaire to access frequency of fish food intake. A total of 1092 men were available for data analysis in this study. Multiple regression models controlling for confounding factors to include frequency of fish food consumption variable were performed to investigate the relationships for OP. Positive correlations between frequency of fish food consumption and T score were reported (β = 0.084, P value = 0.025). Multiple regression analysis indicated that the frequency of fish food consumption was significantly associated with OP (P < 0.05 for model 1 and model 2). The men with high frequency of fish food consumption had a lower prevalence of OP. The findings indicated that frequency of fish food consumption was independently and significantly associated with OP. The prevalence of OP was less frequent in Chinese men preferring fish food habits. ClinicalTrials.gov Identifier: NCT02451397 retrospectively registered 28 May 2015.

Morphometric comparisons of plant-mimetic juvenile fish associated with plant debris observed in the coastal subtropical waters around Kuchierabu-jima Island, southern Japan

PubMed Central

2016-01-01

The general morphological shape of plant-resembling fish and plant parts were compared using a geometric morphometrics approach. Three plant-mimetic fish species, Lobotes surinamensis (Lobotidae), Platax orbicularis (Ephippidae) and Canthidermis maculata (Balistidae), were compared during their early developmental stages with accompanying plant debris (i.e., leaves of several taxa) in the coastal subtropical waters around Kuchierabu-jima Island, closely facing the Kuroshio Current. The degree of similarity shared between the plant parts and co-occurring fish species was quantified, however fish remained morphologically distinct from their plant models. Such similarities were corroborated by analysis of covariance and linear discriminant analysis, in which relative body areas of fish were strongly related to plant models. Our results strengthen the paradigm that morphological clues can lead to ecological evidence to allow predictions of behavioural and habitat choice by mimetic fish, according to the degree of similarity shared with their respective models. The resemblance to plant parts detected in the three fish species may provide fitness advantages via convergent evolutionary effects. PMID:27547571

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

PubMed Central

Sudhagar, Arun; El-Matbouli, Mansour

2018-01-01

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology. PMID:29342931

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

PubMed Central

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-01-01

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

Identification of hydrologic indicators related to fish diversity and abundance: A data mining approach for fish community analysis

NASA Astrophysics Data System (ADS)

Yang, Yi-Chen E.; Cai, Ximing; Herricks, Edwin E.

2008-04-01

This paper develops a new approach to identify hydrologic indicators related to fish community and generate a quantitative function between an ecological target index and the identified hydrologic indicators. The approach is based on genetic programming (GP), a data mining method. Using the Shannon Index (a fish community diversity index) or the number of individuals (total abundance) of a fish community, as an ecological target, the GP identified the most ecologically relevant hydrologic indicators (ERHIs) from 32 indicators of hydrologic alteration, for the case study site, the upper Illinois River. Robustness analysis showed that different GP runs found a similar set of ERHIs; each of the identified ERHI from different GP runs had a consistent relationship with the target index. By comparing the GP results with those from principal component analysis and autecology matrix, the three approaches identified a small number (six) of common ERHIs. Particularly, the timing of low flow (Dmin) seems to be more relevant to the diversity of the fish community, while the magnitude of the low flow (Qb) is more relevant to the total fish abundance; large rising rates result in a significant improvement of fish diversity, which is counterintuitive and against previous findings. The quantitative function developed by GP was further used to construct an indicator impact matrix (IIM), which was demonstrated as a potentially useful tool for streamflow restoration design.

Consistency of individual differences in behaviour of the lion-headed cichlid, Steatocranus casuarius.

PubMed

Budaev, S V; Zworykin, D D; Mochek, A D

1999-11-01

The development of individual differences in behaviour in a novel environment, in the presence of a strange fish and during aggressive interactions with a mirror-image was studied in the lion-headed cichlid (Steatocranus casuarius, Teleostei, Cichlidae). No consistency in behaviour was found at 4-5.5 months of age. However, behaviours scored in situations involving a discrete source of stress (a strange fish or conspecific) become significantly consistent at the age of 12 months. At 4-5.5 but not 12 months of age, larger individuals approached and attacked the strange fish significantly more than smaller ones. These patterns may be associated with development and integration of motivational systems and alternative coping strategies.

Innovative techniques for analyzing the three-dimensional behavioral results from acoustically tagged fish

NASA Astrophysics Data System (ADS)

Steig, Tracey W.; Timko, Mark A.

2005-04-01

Acoustic tags were used to monitor the swimming patterns of downstream migrating salmon smolts approaching various dams on the Columbia River, USA. Downstream migrating yearling chinook (Oncorhynchus tshawytscha), steelhead (Oncorhynchus mykiss), sockeye (Oncorhynchus nerka), and sub-yearling chinook smolts were surgically implanted with acoustic tags. Fish were tracked in three-dimensions as they approached and passed into the turbine intakes, spillways, and surface bypass channel entrances at the dams during the 2004 spring and summer outmigrations. A number of advances in the analysis techniques and software have been made over the past few years. Some of these improvements include the development of various fish density algorithms, stream trace modeling analysis, and advances of three-dimensional animation programs. Three-dimensional tracks of fish approaching the turbine intakes, spillways, and surface bypass channel entrances will be presented. Concentrations of fish passage will be presented as three-dimensional fish densities superimposed over dam structures. Stream trace modeling animation will be presented showing predicted fish passage routes.

Fish Assemblage Response to a Small Dam Removal in the Eightmile River System, Connecticut, USA

NASA Astrophysics Data System (ADS)

Poulos, Helen M.; Miller, Kate E.; Kraczkowski, Michelle L.; Welchel, Adam W.; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Community structure and biogeography of shore fishes in the Gulf of Aqaba, Red Sea

NASA Astrophysics Data System (ADS)

Khalaf, Maroof A.; Kochzius, Marc

2002-02-01

Shore fish community structure off the Jordanian Red Sea coast was determined on fringing coral reefs and in a seagrass-dominated bay at 6 m and 12 m depths. A total of 198 fish species belonging to 121 genera and 43 families was recorded. Labridae and Pomacentridae dominated the ichthyofauna in terms of species richness and Pomacentridae were most abundant. Neither diversity nor species richness was correlated to depth. The abundance of fishes was higher at the deep reef slope, due to schooling planktivorous fishes. At 12 m depth abundance of fishes at the seagrass-dominated site was higher than on the coral reefs. Multivariate analysis demonstrated a strong influence on the fish assemblages by depth and benthic habitat. Fish species richness was positively correlated with hard substrate cover and habitat diversity. Abundance of corallivores was positively linked with live hard coral cover. The assemblages of fishes were different on the shallow reef slope, deep reef slope and seagrass meadows. An analysis of the fish fauna showed that the Gulf of Aqaba harbours a higher species richness than previously reported. The comparison with fish communities on other reefs around the Arabian Peninsula and Indian Ocean supported the recognition of an Arabian subprovince within the Indian Ocean. The affinity of the Arabian Gulf ichthyofauna to the Red Sea is not clear.

Fish assemblage response to a small dam removal in the Eightmile River system, Connecticut, USA.

PubMed

Poulos, Helen M; Miller, Kate E; Kraczkowski, Michelle L; Welchel, Adam W; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

The three-dimensional structure of anosteocytic lamellated bone of fish.

PubMed

Atkins, Ayelet; Reznikov, Natalie; Ofer, Lior; Masic, Admir; Weiner, Steve; Shahar, Ron

2015-02-01

Fish represent the most diverse and numerous of the vertebrate clades. In contrast to the bones of all tetrapods and evolutionarily primitive fish, many of the evolutionarily more advanced fish have bones that do not contain osteocytes. Here we use a variety of imaging techniques to show that anosteocytic fish bone is composed of a sequence of planar layers containing mainly aligned collagen fibrils, in which the prevailing principal orientation progressively spirals. When the sequence of fibril orientations completes a rotation of around 180°, a thin layer of poorly oriented fibrils is present between it and the next layer. The thick layer of aligned fibrils and the thin layer of non-aligned fibrils constitute a lamella. Although both basic components of mammalian lamellar bone are found here as well, the arrangement is unique, and we therefore call this structure lamellated bone. We further show that the lamellae of anosteocytic fish bone contain an array of dense, small-diameter (1-4 μm) bundles of hypomineralized collagen fibrils that are oriented mostly orthogonal to the lamellar plane. Results of mechanical tests conducted on beams from anosteocytic fish bone and human cortical bone show that the fish bones are less stiff but much tougher than the human bones. We propose that the unique lamellar structure and the orthogonal hypomineralized collagen bundles are responsible for the unusual mechanical properties and mineral distribution in anosteocytic fish bone. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Bimanual, intra-operative, fluoroscopy-guided removal of nasopharyngeal migratory fish bone from carotid space.

PubMed

Al-Abduwani, J A; Bhargava, D; Sawhney, S; Al-Abri, R

2010-07-01

We report a rare and unusual case of a patient with an ingested fishbone which migrated from the oropharynx to the anterior compartment of the retropharyngeal space and then to the deep neck space in the nasopharynx (i.e. the carotid space). This report aims to describe a successful, minimally invasive method of foreign body removal which avoided both major skull base surgery and any potential life-threatening complications. A secondary aim is to highlight the role of intra-operative fluoroscopy, an under-used tool. We present a 67-year-old man with a history of fish bone impaction but no fish bone visible on plain X-ray or flexible endoscopy. The diagnosis of fish bone lodged in the retropharyngeal space was confirmed by computed tomography. Surgical exploration of the anterior retropharyngeal space failed to locate the fish bone, as it had migrated to a new, unknown location. Intra-operative fluoroscopy was vital for the removal of the fish bone, as it was impossible to see with the naked eye and had migrated from its previously imaged position. The fish bone was finally retrieved bimanually using external pressure on the submandibular region, which displaced the fish bone, and fluoroscopic guidance, which assisted its removal from the nasopharyngeal lumen. To the best of our knowledge, this is the first reported case of bimanual, intra-operative, fluoroscopy-guided, intra-luminal removal of a migratory fish bone from the deep neck space in this region of the nasopharynx.

Comparative analysis of EPA and DHA in fish oil nutritional capsules by GC-MS.

PubMed

Yi, Tao; Li, Shuk-Man; Fan, Jia-Yi; Fan, Lan-Lan; Zhang, Zhi-Feng; Luo, Pei; Zhang, Xiao-Jun; Wang, Jian-Gang; Zhu, Lin; Zhao, Zhong-Zhen; Chen, Hu-Biao

2014-12-13

Fish oil is a popular nutritional product consumed in Hong Kong. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are the two main bioactive components responsible for the health benefits of fish oil. Market survey in Hong Kong demonstrated that various fish oil capsules with different origins and prices are sold simultaneously. However, these capsules are labelled with same ingredient levels, namely EPA 180 mg/g and DHA 120 mg/g. This situation makes the consumers very confused. To evaluate the quality of various fish oil capsules, a comparative analysis of the contents of EPA and DHA in fish oil is crucial. A gas chromatography-mass spectrometry (GC-MS) method was developed for identification and determination of EPA and DHA in fish oil capsules. A comprehensive validation of the developed method was conducted. Ten batches of fish oil capsules samples purchased from drugstores of Hong Kong were analyzed by using the developed method. The present method presented good sensitivity, precision and accuracy. The limits of detection (LOD) for EPA and DHA were 0.08 ng and 0.21 ng, respectively. The relative standard deviation (RSD) values of EPA and DHA for repeatability tests were both less than 1.05%; and the recovery for accuracy test of EPA and DHA were 100.50% and 103.83%, respectively. In ten fish oil samples, the contents of EPA ranged from 39.52 mg/g to 509.16 mg/g, and the contents of DHA ranged from 35.14 mg/g to 645.70 mg/g. The present method is suitable for the quantitative analysis of EPA and DHA in fish oil capsules. There is a significant variation in the contents of the quantified components in fish oil samples, and there is not a linear relationship between price and contents of EPA and DHA. Strict supervision of the labelling of the fish oil capsules is urgently needed.

Fish consumption and risk of gastrointestinal cancers: A meta-analysis of cohort studies

PubMed Central

Yu, Xiao-Feng; Zou, Jian; Dong, Jie

2014-01-01

AIM: To assess quantitatively the relationship between fish intake and the incidence of gastrointestinal cancers in a meta-analysis of cohort studies. METHODS: We searched MEDLINE, Embase, Science Citation Index Expanded, and the bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs) and corresponding 95% confidence intervals (CIs) of various cancers with respect to fish intake. When RRs were not available in the published article, they were computed from the exposure distributions. Two investigators extracted the data independently and discrepancies were resolved by discussion with a third investigator. We performed random-effect meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with a 20-g/d increment of fish consumption. RESULTS: Forty-two studies, comprising 27 independent cohorts, met our inclusion criteria. The studies included 2325040 participants and 24115 incident cases of gastrointestinal cancer, with an average follow-up of 13.6 years. Compared with individuals who did not eat, or seldom ate, fish, the pooled RR of gastrointestinal cancers was 0.93 (95%CI: 0.88-0.98) for regular fish consumers, 0.94 (0.89-0.99) for low to moderate fish consumers, and 0.91 (0.84-0.97) for high fish consumers. Overall, a 20-g increase in fish consumption per day was associated with a 2% reduced risk of gastrointestinal cancers (RR = 0.98; 95%CI: 0.96-1.01). In subgroup analyses, we noted that fish consumption was associated with reduced risk of colorectal (RR = 0.93; 95%CI: 0.87-0.99; P < 0.01), esophageal (RR = 0.91; 95%CI: 0.83-0.99; P < 0.05) and hepatocellular cancers (RR = 0.71; 95%CI: 0.48-0.95; P < 0.01). CONCLUSION: This meta-analysis suggested that fish consumption may reduce total gastrointestinal cancer incidence. Inverse relationships were also detected between fish consumption and specific types of cancers. PMID:25386090

Chemical analysis of fish bile extracts for monitoring endocrine disrupting chemical exposure in water: Bisphenol A, alkylphenols, and norethindrone.

PubMed

Wu, Minghong; Pan, Chenyuan; Yang, Ming; Xu, Bentuo; Lei, Xiangjie; Ma, Jing; Cai, Ling; Chen, Jingsi

2016-01-01

The present study determined concentrations of estrogenic bisphenol A (BPA), nonylphenol, octylphenol (4-tert-octylphenol), butylphenol (4-tert-butylphenol), and progestogenic norethindrone by liquid chromatography-tandem mass spectrometry in bile extracts from field fish from the Xin'an River and market fish in Shanghai, China. Compared with the field fish, endocrine disrupting chemical (EDC) concentrations in market fish bile were at relatively high levels with high detectable rates. The average concentrations of BPA, nonylphenol, 4-tert-octylphenol, 4-tert-butylphenol, and norethindrone in field fish bile were 30.1 µg/L, 203 µg/L, 4.69 µg/L, 7.84 µg/L, and 0.514 µg/L, respectively; in market fish bile they were 240 µg/L, 528 µg/L, 76.5 µg/L, 12.8 µg/L, and 5.26 µg/L, respectively; and in the surface water of Xin'an River they were 38.8 ng/L, 7.91 ng/L, 1.98 ng/L, 2.66 ng/L, and 0.116 ng/L, respectively. The average of total estrogenic activity of river water was 3.32 ng/L estradiol equivalents. High bioconcentration factors (BCFs) were discovered for all 5 EDCs (≧998-fold) in field fish bile. Furthermore, the authors analyzed the BCF value of BPA in fish bile after 30-d exposure to environmentally relevant concentrations of BPA in the laboratory, and the analysis revealed that BCF in fish bile (BCF(Fish bile)) changed in an inverse concentration-dependent manner based on the log10-transformed BPA concentration in water. Strikingly, the data from the field study were well fitted within this trend. The data together suggested that analysis of fish bile extracts could be an efficient method for assessing waterborne EDCs exposure for aquatic biota. © 2015 SETAC.

Fish consumption and risk of gastrointestinal cancers: a meta-analysis of cohort studies.

PubMed

Yu, Xiao-Feng; Zou, Jian; Dong, Jie

2014-11-07

To assess quantitatively the relationship between fish intake and the incidence of gastrointestinal cancers in a meta-analysis of cohort studies. We searched MEDLINE, Embase, Science Citation Index Expanded, and the bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs) and corresponding 95% confidence intervals (CIs) of various cancers with respect to fish intake. When RRs were not available in the published article, they were computed from the exposure distributions. Two investigators extracted the data independently and discrepancies were resolved by discussion with a third investigator. We performed random-effect meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with a 20-g/d increment of fish consumption. Forty-two studies, comprising 27 independent cohorts, met our inclusion criteria. The studies included 2325040 participants and 24115 incident cases of gastrointestinal cancer, with an average follow-up of 13.6 years. Compared with individuals who did not eat, or seldom ate, fish, the pooled RR of gastrointestinal cancers was 0.93 (95%CI: 0.88-0.98) for regular fish consumers, 0.94 (0.89-0.99) for low to moderate fish consumers, and 0.91 (0.84-0.97) for high fish consumers. Overall, a 20-g increase in fish consumption per day was associated with a 2% reduced risk of gastrointestinal cancers (RR = 0.98; 95%CI: 0.96-1.01). In subgroup analyses, we noted that fish consumption was associated with reduced risk of colorectal (RR = 0.93; 95%CI: 0.87-0.99; P < 0.01), esophageal (RR = 0.91; 95%CI: 0.83-0.99; P < 0.05) and hepatocellular cancers (RR = 0.71; 95%CI: 0.48-0.95; P < 0.01). This meta-analysis suggested that fish consumption may reduce total gastrointestinal cancer incidence. Inverse relationships were also detected between fish consumption and specific types of cancers.

Studying the Variability of Bright Stars with the CONCAM Sky Monitoring Network

NASA Astrophysics Data System (ADS)

Pereira, W. E.; Nemiroff, R. J.; Rafert, J. B.; Perez-Ramirez, D.

2001-12-01

CONCAMs have now been deployed at some of the world's major observatories including KPNO in Arizona, Mauna Kea in Hawaii, and Wise Observatory in Israel. Data from these mobile, inexpensive and continuous sky cameras, consisting of a fish-eye lens mated to a CCD camera and run by a laptop, has been ever-increasing. Initial efforts to carry out photometric analysis of CONCAM fits images have now been fortified by a more automated technique of analyzing this data. Results of such analyses - variability of several bright stars, in particular, are presented, as well as the use of these cameras as cloud monitors to remote observers.

Imaging dipole flow sources using an artificial lateral-line system made of biomimetic hair flow sensors

PubMed Central

Dagamseh, Ahmad; Wiegerink, Remco; Lammerink, Theo; Krijnen, Gijs

2013-01-01

In Nature, fish have the ability to localize prey, school, navigate, etc., using the lateral-line organ. Artificial hair flow sensors arranged in a linear array shape (inspired by the lateral-line system (LSS) in fish) have been applied to measure airflow patterns at the sensor positions. Here, we take advantage of both biomimetic artificial hair-based flow sensors arranged as LSS and beamforming techniques to demonstrate dipole-source localization in air. Modelling and measurement results show the artificial lateral-line ability to image the position of dipole sources accurately with estimation error of less than 0.14 times the array length. This opens up possibilities for flow-based, near-field environment mapping that can be beneficial to, for example, biologists and robot guidance applications. PMID:23594816

RNA-FISH to Study Regulatory RNA at the Site of Transcription.

PubMed

Soler, Marta; Boque-Sastre, Raquel; Guil, Sonia

2017-01-01

The increasing role of all types of regulatory RNAs in the orchestration of cellular programs has enhanced the development of a variety of techniques that allow its precise detection, quantification, and functional scrutiny. Recent advances in imaging and fluoresecent in situ hybridization (FISH) methods have enabled the utilization of user-friendly protocols that provide highly sensitive and accurate detection of ribonucleic acid molecules at both the single cell and subcellular levels. We herein describe the approach originally developed by Stellaris ® , in which the target RNA molecule is fluoresecently labeled with multiple tiled complementary probes each carrying a fluorophore, thus improving sensitivity and reducing the chance of false positives. We have applied this method to the detection of nascent RNAs that partake of special regulatory structures called R loops. Their growing role in active gene expression regulation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012; Ginno et al., Mol Cell 45:814-825, 2012; Sun et al., Science 340:619-621, 2013; Bhatia et al., Nature 511:362-365, 2014) imposes the use of a combination of in vivo and in vitro techniques for the detailed analysis of the transcripts involved. Therefore, their study is a good example to illustrate how RNA FISH, combined with transcriptional arrest and/or cell synchronization, permits localization and temporal characterization of potentially regulatory RNA sequences.

Morphological correlates of swimming activity in wild largemouth bass (Micropterus salmoides) in their natural environment.

PubMed

Hanson, K C; Hasler, C T; Suski, C D; Cooke, S J

2007-12-01

Individual variation in morphology has been linked to organismal performance in numerous taxa. Recently, the relationship between functional morphology and swimming performance in teleost fishes has been studied in laboratory experiments. In this study, we evaluate the relationship between morphology and swimming activity of wild largemouth bass (Micropterus salmoides) during the reproductive period, providing the first data derived on free-swimming fish not exposed to forced swim trials in the laboratory. Sixteen male largemouth bass were angled from their nests, telemetered, and subsequently monitored by a whole-lake acoustic hydrophone array with sub-meter accuracy. Additionally, eleven morphological measurements were taken from digital images of each fish. A principal components analysis of the morphological measurements described 79.8% of the variance. PC1 was characterized by measures of overall body stoutness, PC2 was characterized by measures of the length and depth of the caudal region, and PC3 characterized individuals with relatively large anterior portions of the body and relatively small caudal areas. Of these variables, only PC3 showed significant relationships to swimming activity throughout the parental care period. PC3 was negatively correlated with multiple measures of swimming activity across the parental care period. Furthermore, swimming performance of individual male bass was noted to be repeatable across the parental care period indicating that this phenomenon extends beyond the laboratory.

The Electric Field of a Weakly Electric Fish

NASA Astrophysics Data System (ADS)

Rasnow, Brian K.

Freshwater fish of the genus Apteronotus (family Gymnotidae) generate a weak, high frequency electric field (<100 mV/cm, 0.5-10 kHz) which permeates their local environment. These nocturnal fish are acutely sensitive to perturbations in their electric field caused by other electric fish, and nearby objects whose impedance is different from the surrounding water. This thesis presents high temporal and spatial resolution maps of the electric potential and field on and near Apteronotus. The fish's electric field is a complicated and highly stable function of space and time. Its characteristics, such as spectral composition, timing, and rate of attenuation, are examined in terms of physical constraints, and their possible functional roles in electroreception. Temporal jitter of the periodic field is less than 1 musec. However, electrocyte activity is not globally synchronous along the fish's electric organ. The propagation of electrocyte activation down the fish's body produces a rotation of the electric field vector in the caudal part of the fish. This may assist the fish in identifying nonsymmetrical objects, and could also confuse electrosensory predators that try to locate Apteronotus by following its fieldlines. The propagation also results in a complex spatiotemporal pattern of the EOD potential near the fish. Visualizing the potential on the same and different fish over timescales of several months suggests that it is stable and could serve as a unique signature for individual fish. Measurements of the electric field were used to calculate the effects of simple objects on the fish's electric field. The shape of the perturbation or "electric image" on the fish's skin is relatively independent of a simple object's size, conductivity, and rostrocaudal location, and therefore could unambiguously determine object distance. The range of electrolocation may depend on both the size of objects and their rostrocaudal location. Only objects with very large dielectric constants cause appreciable phase shifts, and these are strongly dependent on the water conductivity.

A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

USGS Publications Warehouse

Adams, Noah S.; Hatton, Tyson W.

2012-01-01

Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To facilitate comparison among species in this report, we combined JBS and turbine passage for yearling Chinook salmon, steelhead, and subyearling Chinook salmon even though we were able to differentiate between passage through the JBS or turbines for these three species. Information on passage proportions through the JBS and turbines can be found in the first report. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, within the powerhouse region, passage proportions among the three powerhouse areas were often greater in the southern and middle areas of the powerhouse compared to the northern area of the powerhouse for yearling and subyearling Chinook salmon. The opposite generally was observed for steelhead. The results of this analysis also allowed us to confirm and quantify the extent of milling behavior that was observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the dam. In comparison, greater than 0.20 of the Chinook salmon passed within each of the powerhouse areas. Less milling behavior was observed for all species for fish that first approached the spillway. Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and fewer transitioned to adjoining areas in the powerhouse. In addition to quantifying what had been previously speculated about the behavior of fish in the forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and passage can be influenced by changes to the operations and structure of McNary Dam. For example, the addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been reported showing that TSWs increased passage through non-turbine routes and the fish-track videos indicated, in general, how fish behaved before passing the TSWs. However, the analysis presented in this report allowed us to better understand how fish transitioned across the face of the dam before passing the TSWs and resulted in a quantitative way to measure the effect of moving the location of the TSWs from year to year. Installation of the TSWs in bays 22 and 20 clearly increased passage proportions through the southern one-third of the spillway area for all species, most significantly for steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007. Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased the number of fish that transitioned to adjoining areas before passing the dam. Perhaps the most interesting new information to come out of the two-step Markov chain analysis relates to how the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the highest proportion of fish passing through TSW 22 was for fish that transitioned from the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW 20 after coming from the powerhouse area. Instead, the proportion of fish that passed TSW 20 after coming from the northern part of the spillway was twice as high as the proportion of fish that passed through TSW 20 after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 22, the proportion of fish passing through TSW 20 after coming from the powerhouse was higher than the proportion of fish passing TSW 20 after coming from the northern part of the spillway. Passage proportions for fish passing through TSW 19, the farthest north of the two TSWs during 2008, was higher for fish that came from the northern part of the spillway compared to the proportion of fish that passed through TSW 19 after coming from the powerhouse. The Markov chain analysis provided a mathematical way to characterize fish behavior in the forebay of McNary Dam and helped refine our understanding of how fish movements were influenced by operational and structural changes at the dam. The numerical information used to quantify the behavior of fish also can be used to construct simulations to examine how proposed fish passage structures might influence passage of juvenile salmonids. To demonstrate this, we used the results of the Markov chain analysis to examine how a virtual fish collector located in the center of the powerhouse might influence passage of juvenile salmonids at McNary Dam.

The Independent Technical Analysis Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duberstein, Corey A.; Ham, Kenneth D.; Dauble, Dennis D.

2007-04-13

The Bonneville Power Administration (BPA) contracted with the Pacific Northwest National Laboratory (PNNL) to provide technical analytical support for system-wide fish passage information (BPA Project No. 2006-010-00). The goal of this project was to produce rigorous technical analysis products using independent analysts and anonymous peer reviewers. In the past, regional parties have interacted with a single entity, the Fish Passage Center to access the data, analyses, and coordination related to fish passage. This project provided an independent technical source for non-routine fish passage analyses while allowing routine support functions to be performed by other well-qualified entities.

Fires, East Falkland Island, South Atlantic

NASA Technical Reports Server (NTRS)

2007-01-01

This near-nadir image (looking almost straight down) of the Falkland Islands in the South Atlantic was acquired at the southernmost extent of the International Space Station's latitudinal orbit range of approximately 52 degrees north to 52 degrees south relative to the surface of the Earth. The windy and relatively dry climate, which includes roughly 600 millimeters (24 inches) of precipitation annually, has given rise to natural vegetation comprised of treeless grassland with scattered bogs. The grasslands are ideal for sheep rearing--the dominant occupation until recent decades, when fishing (mainly squid for Spain) and tourism became the mainstays of the economy. These expanses of grassland provide ready fuel for fires, as indicated by the several long smoke plumes visible in this astronaut photograph. Astronaut photograph ISS015-E-30526 was acquired on September 25, 2007, with a Kodak 760C digital camera fitted with a 58 mm lens. The image was taken by the Expedition 15 crew, and is provided by the ISS Crew Earth Observations experiment and Image Science and Analysis Laboratory, Johnson Space Center. The image in this article has been cropped and enhanced to improve contrast. Lens artifacts have been removed.

Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

PubMed

Malek, A J; Collie, J S; Taylor, D L

2016-09-01

A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles. © 2016 The Fisheries Society of the British Isles.

Fish consumption and CHD mortality: an updated meta-analysis of seventeen cohort studies.

PubMed

Zheng, Jusheng; Huang, Tao; Yu, Yinghua; Hu, Xiaojie; Yang, Bin; Li, Duo

2012-04-01

Results of studies on fish consumption and CHD mortality are inconsistent. The present updated meta-analysis was conducted to investigate the up-to-date pooling effects. A random-effects model was used to pool the risk estimates. Generalized least-squares regression and restricted cubic splines were used to assess the possible dose-response relationship. Subgroup analyses were conducted to examine the sources of heterogeneity. PubMed and ISI Web of Science databases up to September 2010 were searched and secondary referencing qualified for inclusion in the study. Seventeen cohorts with 315,812 participants and average follow-up period of 15·9 years were identified. Compared with the lowest fish intake (<1 serving/month or 1-3 servings/month), the pooled relative risk (RR) of fish intake on CHD mortality was 0·84 (95% CI 0·75, 0·95) for low fish intake (1 serving/week), 0·79 (95% CI 0·67, 0·92) for moderate fish intake (2-4 servings/week) and 0·83 (95% CI 0·68, 1·01) for high fish intake (>5 servings/week). The dose-response analysis indicated that every 15 g/d increment of fish intake decreased the risk of CHD mortality by 6% (RR = 0·94; 95% CI 0·90, 0·98). The method of dietary assessment, gender and energy adjustment affected the results remarkably. Our results indicate that either low (1 serving/week) or moderate fish consumption (2-4 servings/week) has a significantly beneficial effect on the prevention of CHD mortality. High fish consumption (>5 servings/week) possesses only a marginally protective effect on CHD mortality, possibly due to the limited studies included in this group.

Transcriptomic analyses of tributyltin-induced sexual dimorphisms in rare minnow (Gobiocypris rarus) brains.

PubMed

Zhang, Ji-Liang; Liu, Min; Zhang, Chun-Nuan; Li, Er-Chao; Fan, Ming-Zhen; Huang, Mao-Xian

2018-07-30

The brain of fish displays sexual dimorphisms and exhibits remarkable sexual plasticity throughout their life span. Although reproductive toxicity of tributyltin (TBT) in fish is well documented in fish, it remains unknown whether TBT interrupts sexual dimorphisms of fish brains. In this work, brain transcriptomic profiles of rare minnow (Gobiocypris rarus) was characterized and sex-biased genes were identified using RNA sequencing. Functional annotation and enrichment analysis were performed to reveal differences of gene products and pathways between the brains of male and female fish. Furthermore, transcriptomic responses of male and female brains to TBT at 10 ng/L were also investigated to understand effects of TBT on brain sexual dimorphisms. Only 345 male-biased and 273 female-biased genes were found in the brains. However, significant female-biased pathways of circadian rhythm and phototransduction were identified in the brains by enrichment analysis. Interestingly, following TBT exposure in the female fish, the circadian rhythm pathway was significantly disrupted based on enrichment analysis, while in the male fish, the phototransduction pathway was significantly disrupted. In the female fish, expression of genes (Per, Cry, Rev-Erb α, Ror, Dec and CK1δ/ε) in the circadian rhythm pathway was down-regulated after TBT exposure; while in the male fish, expression of genes (Rec, GNAT1_2, GNGT1, Rh/opsin, PDE and Arr) in the phototransduction pathway was up-regulated after TBT exposure. Overall, our results not only provide key data on the molecular basis of brain sexual dimorphisms in fish, but also offer valuable resources for investigating molecular mechanisms by which environmental chemicals might influence brain sexual plasticity. Copyright © 2018 Elsevier Inc. All rights reserved.

A new compact, cost-efficient concept for underwater range-gated imaging: the UTOFIA project

NASA Astrophysics Data System (ADS)

Mariani, Patrizio; Quincoces, Iñaki; Galparsoro, Ibon; Bald, Juan; Gabiña, Gorka; Visser, Andy; Jónasdóttir, Sigrun; Haugholt, Karl Henrik; Thorstensen, Jostein; Risholm, Petter; Thielemann, Jens

2017-04-01

Underwater Time Of Flight Image Acquisition system (UTOFIA) is a recently launched H2020 project (H2020 - 633098) to develop a compact and cost-effective underwater imaging system especially suited for observations in turbid environments. The UTOFIA project targets technology that can overcome the limitations created by scattering, by introducing cost-efficient range-gated imaging for underwater applications. This technology relies on a image acquisition principle that can extends the imaging range of the cameras 2-3 times respect to other cameras. Moreover, the system will simultaneously capture 3D information of the observed objects. Today range-gated imaging is not widely used, as it relies on specialised optical components making systems large and costly. Recent technology developments have made it possible a significant (2-3 times) reduction in size, complexity and cost of underwater imaging systems, whilst addressing the scattering issues at the same time. By acquiring simultaneous 3D data, the system allows to accurately measure the absolute size of marine life and their spatial relationship to their habitat, enhancing the precision of fish stock monitoring and ecology assessment, hence supporting proper management of marine resources. Additionally, the larger observed volume and the improved image quality make the system suitable for cost-effective underwater surveillance operations in e.g. fish farms, underwater infrastructures. The system can be integrated into existing ocean observatories for real time acquisition and can greatly advance present efforts in developing species recognition algorithms, given the additional features provided, the improved image quality and the independent illumination source based on laser. First applications of the most recent prototype of the imaging system will be provided including inspection of underwater infrastructures and observations of marine life under different environmental conditions.

Bacterial Pollution Indicators in the Intestinal Tract of Freshwater Fish

PubMed Central

Geldreich, Edwin E.; Clarke, Norman A.

1966-01-01

A study was made of the occurrence, distribution, and persistence of coliforms, fecal coliforms, and fecal streptococci in the intestinal tract of freshwater fish. A total of 132 fish representing 14 different species were used in various phases of these experiments. Examination of the intestinal contents of 78 fish from moderately polluted sections of the Little Miami River indicated that fecal coliform densities were lowest in bluegills (less than 20 per gram) and highest in catfish (1,090,000 per gram). Levels of fecal streptococci for these two species were 220 and 240,000 per gram, respectively. The occurrence of fecal coliforms in fish caught in this stream reflected the warm-blooded-animal-pollution level of the water. All fish used in this phase of the study were caught during July, August, and September when the water temperatures were between 13 and 18 C. The fate of fecal coliforms and Streptococcus faecalis in the fish intestine indicated that these organisms can probably survive and multiply when fish and water temperatures are 20 C or higher, but only when the organisms are retained in the gut for periods beyond 24 hr. Based on the biochemical reactions for 3,877 coliform strains isolated from 132 freshwater fish of 14 different species, 91.4% of all strains were composed of five IMViC types. In a similar study of the biochemical reactions of 850 streptococci isolated from the intestinal tract of 55 freshwater fish, the predominant strains included S. faecalis and various closely associated biotypes. No consistently recurring pattern for either coliforms or streptococci could be developed to identify species of fish investigated. The composition of the intestinal flora is, however, related in varying degree to the level of contamination of water and food in the environment. Images Fig. 1 Fig. 2 PMID:6008184

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

PubMed Central

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S.

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome PMID:26980518

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome. © The Author(s) 2016. Published by Oxford University Press.

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

USGS Publications Warehouse

Luczkovich, J.J.; Ward, G.P.; Johnson, J.C.; Christian, R.R.; Baird, D.; Neckles, H.; Rizzo, W.M.

2002-01-01

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa present in Halodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity ??? 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers, and piscivores. These trophic groups, cross-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.

Chromosomal analysis of blastocyst derived from monopronucleated ICSI zygotes: approach by double trophectoderm biopsy.

PubMed

Mateo, Silvia; Vidal, Francesca; Coll, Lluc; Veiga, Anna; Boada, Montserrat

2017-09-01

This study aims to increase the knowledge about monopronucleated ICSI-derived blastocysts, analyzing trophectoderm biopsies by aCGH and FISH to evaluate their chromosome constitution. Fifteen monopronucleated ICSI-derived blastocysts were studied. Double trophectoderm biopsy was performed and analyzed by FISH and aCGH. The blastocysts were classified according to chromosome constitution. Disagreements between the two techniques were assessed. Results obtained after FISH and aCGH analyses showed the following: 20% (3/15) and 60% (9/15) diploid females, respectively; 26.7% (4/15) and 26.7% (4/15) diploid males, respectively; and 53.3% (8/15) and 13.3% (2/15) mosaics, respectively. No mosaic male embryos were found using FISH or aCGH. There were disagreements in 40% (6/15) of the cases due to the higher detection of mosaicism by FISH compared to aCGH. The combination of FISH and aCGH has been shown to be a suitable approach to increase the knowledge about monopronucleated ICSI-derived embryos. FISH analysis of blastocysts derived from monopronucleated ICSI zygotes enabled us to conclude that aCGH underestimates haploidy. Some diploid embryos diagnosed by aCGH are in fact mosaic. In cases where these embryos would be used for reproductive purposes, extra analysis of parental genome origin is recommended.

Poultry and fish intake and risk of esophageal cancer: A meta-analysis of observational studies.

PubMed

Jiang, Gengxi; Li, Bailing; Liao, Xiaohong; Zhong, Chongjun

2016-03-01

Mixed results regarding the association between white meat (including poultry and fish) intake and the risk of esophageal cancer (EC) have been reported. We performed a meta-analysis to provide a quantitative assessment of this association. Relevant studies were identified in MEDLINE until December 31, 2012. Summary relative risks (SRRs) with 95% confidence intervals (CIs) were pooled with a random-effects model. A total of 20 articles, including 3990 cases with EC, were included in this meta-analysis. Compared to individuals with the lowest level of fish intake, individuals with the highest fish intake were found to have reduced risk of EC (SRRs = 0.69; 95% CIs: 0.57-0.85), while poultry intake was not associated with EC (SRRs = 0.83; 95% CIs: 0.62-1.12). Total fish consumption is associated with reduced esophageal squamous cell carcinoma (ESCC) risk, while poultry consumption was not associated with ESCC risk. Additionally, neither poultry nor fish consumption was associated with esophageal adenocarcinoma risk. Our results suggest that fish consumption may have a potential role in EC prevention, while poultry intake has no effect. However, because the majority of data was from case-control studies, further well-designed prospective studies are warranted. © 2013 Wiley Publishing Asia Pty Ltd.

Repeatability, Reproducibility, Separative Power and Subjectivity of Different Fish Morphometric Analysis Methods

PubMed Central

Takács, Péter

2016-01-01

We compared the repeatability, reproducibility (intra- and inter-measurer similarity), separative power and subjectivity (measurer effect on results) of four morphometric methods frequently used in ichthyological research, the “traditional” caliper-based (TRA) and truss-network (TRU) distance methods and two geometric methods that compare landmark coordinates on the body (GMB) and scales (GMS). In each case, measurements were performed three times by three measurers on the same specimen of three common cyprinid species (roach Rutilus rutilus (Linnaeus, 1758), bleak Alburnus alburnus (Linnaeus, 1758) and Prussian carp Carassius gibelio (Bloch, 1782)) collected from three closely-situated sites in the Lake Balaton catchment (Hungary) in 2014. TRA measurements were made on conserved specimens using a digital caliper, while TRU, GMB and GMS measurements were undertaken on digital images of the bodies and scales. In most cases, intra-measurer repeatability was similar. While all four methods were able to differentiate the source populations, significant differences were observed in their repeatability, reproducibility and subjectivity. GMB displayed highest overall repeatability and reproducibility and was least burdened by measurer effect. While GMS showed similar repeatability to GMB when fish scales had a characteristic shape, it showed significantly lower reproducability (compared with its repeatability) for each species than the other methods. TRU showed similar repeatability as the GMS. TRA was the least applicable method as measurements were obtained from the fish itself, resulting in poor repeatability and reproducibility. Although all four methods showed some degree of subjectivity, TRA was the only method where population-level detachment was entirely overwritten by measurer effect. Based on these results, we recommend a) avoidance of aggregating different measurer’s datasets when using TRA and GMS methods; and b) use of image-based methods for morphometric surveys. Automation of the morphometric workflow would also reduce any measurer effect and eliminate measurement and data-input errors. PMID:27327896

CLOSED-LOOP STRIPPING ANALYSIS (CLSA) OF SYNTHETIC MUSK COMPOUNDS FROM FISH TISSUES WITH MEASUREMENT BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY WITH SELECTED-ION MONITORING

EPA Science Inventory

Synthetic musk compounds have been found in surface water, fish tissues, and human breast milk. Current techniques for separating these compounds from fish tissues require tedious sample clean-upprocedures A simple method for the deterrnination of these compounds in fish tissues ...

Socio-Economics of Lake Victoria's Fisheries: An Analysis of the Shifting Roles and Status of Women Fish Traders

ERIC Educational Resources Information Center

Craig, Heather

2007-01-01

Fishing industries around the world are currently undergoing a process of industrialization and commercialization. A similar story is unfolding in many fishing communities: large-scale industrial fishers who possess enormous capital and advanced technologies are threatening the lives of small-scale fisherfolk. The fishing industry in Lake Victoria…

A pressure-based force and torque prediction technique for the study of fish-like swimming

PubMed Central

Dabiri, John O.; Lauder, George V.

2017-01-01

Many outstanding questions about the evolution and function of fish morphology are linked to swimming dynamics, and a detailed knowledge of time-varying forces and torques along the animal’s body is a key component in answering many of these questions. Yet, quantifying these forces and torques experimentally represents a major challenge that to date prevents a full understanding of fish-like swimming. Here, we develop a method for obtaining these force and torque data non-invasively using standard 2D digital particle image velocimetry in conjunction with a pressure field algorithm. We use a mechanical flapping foil apparatus to model fish-like swimming and measure forces and torques directly with a load cell, and compare these measured values to those estimated simultaneously using our pressure-based approach. We demonstrate that, when out-of-plane flows are relatively small compared to the planar flow, and when pressure effects sufficiently dominate shear effects, this technique is able to accurately reproduce the shape, magnitude, and timing of locomotor forces and torques experienced by a fish-like swimmer. We conclude by exploring of the limits of this approach and its feasibility in the study of freely-swimming fishes. PMID:29216264

The Impact of Marine Protected Areas on Reef-Wide Population Structure and Fishing-Induced Phenotypes in Coral-Reef Fishes

NASA Astrophysics Data System (ADS)

Fidler, Robert Young, III

Overfishing and destructive fishing practices threaten the sustainability of fisheries worldwide. In addition to reducing population sizes, anthropogenic fishing effort is highly size-selective, preferentially removing the largest individuals from harvested stocks. Intensive, size-selective mortality induces widespread phenotypic shifts toward the predominance of smaller and earlier-maturing individuals. Fish that reach sexual maturity at smaller size and younger age produce fewer, smaller, and less viable larvae, severely reducing the reproductive capacity of exploited populations. These directional phenotypic alterations, collectively known as "fisheries-induced evolution" (FIE) are among the primary causes of the loss of harvestable fish biomass. Marine protected areas (MPAs) are one of the most widely utilized components of fisheries management programs around the world, and have been proposed as a potential mechanism by which the impacts of FIE may be mitigated. The ability of MPAs to buffer exploited populations against fishing pressure, however, remains debated due to inconsistent results across studies. Additionally, empirical evidence of phenotypic shifts in fishes within MPAs is lacking. This investigation addresses both of these issues by: (1) using a categorical meta-analysis of MPAs to standardize and quantify the magnitude of MPA impacts across studies; and (2) conducting a direct comparison of life-history phenotypes known to be influenced by FIE in six reef-fish species inside and outside of MPAs. The Philippines was used as a model system for analyses due to the country's significance in global marine biodiversity and reliance on MPAs as a fishery management tool. The quantitative impact of Philippine MPAs was assessed using a "reef-wide" meta-analysis. This analysis used pooled visual census data from 39 matched pairs of MPAs and fished reefs surveyed twice over a mean period of 3 years. In 17 of these MPAs, two additional surveys were conducted using size-specific fish counts, allowing for spatiotemporal comparisons of abundance and demographic structure of fish populations across protected and fished areas. Results of the meta-analysis revealed that: (1) although fish density was higher inside MPAs than in fished reefs at each sampling period, reef-wide density often increased or remained stable over time; and (2) increases in large-bodied fish were evident reef-wide between survey periods, indicating that positive demographic shifts occurred simultaneously in both MPAs and adjacent areas. Increases in large-bodied fish were observed across a range of taxa, but were most prominent in families directly targeted by fishermen. These results suggest that over relatively few years of protection, Philippine MPAs promoted beneficial shifts in population structure throughout entire reef systems, rather than simply maintaining stable populations within their borders. Relationships between MPA age and shifts in fish density or demographic structure were rare, but may have been precluded by the relatively short period between replicate surveys. Although increases in fish density inside MPAs were occasionally associated with MPA size, there were no significant relationships between the size of MPAs and reef-wide increases in fish density. The reef-wide framework of MPA assessment used in this study has the advantage of treating MPAs and fished reefs as an integrated system, thus revealing trends that would be indistinguishable in traditional spatial comparisons between MPAs and fished reefs. The impact of MPAs on fishing-induced life-history traits was assessed by comparing growth and maturation patterns exhibited by six reef-fish species inside and outside five MPAs and adjacent, fished reefs in Zambales, Luzon, Philippines. This analysis demonstrated considerable variation in terminal body-sizes (Linf) and growth rates (K) between conspecifics in MPAs and fished reefs. Three of the four experimental species directly targeted for food in the region (Acanthurus nigrofuscus, Ctenochaetus striatus, and Parupeneus multifasciatus) exhibited greater Linf, lower K, or both characteristics inside at least one MPA compared to populations in adjacent, fished reefs. Life-history shifts were concentrated in the oldest and largest MPAs, but occurred at least once in each of the five MPAs that were examined. A fourth species harvested for food (Ctenochaetus binotatus), as well as a species targeted for the aquarium trade (Zebrasoma scopas) and a non-target species (Plectroglyphidodon lacrymatus) did not exhibit differential phenotypes between MPAs and fished reefs. The relatively high frequency of alterations to life-history characteristics across MPAs in harvested species suggests that observed changes in the density and size-structure of harvested fish populations inside MPAs are likely driven by spatial disparities in fishing pressure, and are the result of phenotypic changes rather than increased longevity.

Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

2017-04-01

Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for the acquisition of correlative information on microorganisms within their respective habitats.

High-throughput, image-based screening of pooled genetic variant libraries

PubMed Central

Emanuel, George; Moffitt, Jeffrey R.; Zhuang, Xiaowei

2018-01-01

Image-based, high-throughput screening of genetic perturbations will advance both biology and biotechnology. We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in numerous individual cells. We achieve genotyping by introducing barcoded genetic variants into cells and using massively multiplexed FISH to measure the barcodes. We demonstrated this method by screening mutants of the fluorescent protein YFAST, yielding brighter and more photostable YFAST variants. PMID:29083401

From static electric images to electric flow: towards dynamic perceptual cues in active electroreception.

PubMed

Hofmann, Volker; Sanguinetti-Scheck, Juan I; Gómez-Sena, Leonel; Engelmann, Jacob

2013-01-01

Active electroreception is an ancestral trait found in many aquatic vertebrates and has evolved independently in two teleost lineages, the Gymnotiformes and the Mormyriformes. Unique to these so-called weakly electric fish is their ability to actively generate electrical currents in the water and sense the electrical properties of the environment. How natural behavior contributes to this sensory system has been of interest to neuroethologists since the pioneering works of Lissmann. Here we report on a mutual modeling and experimental study of the stimuli available during active electrolocation of Gnathonemus petersii (Mormyridae). We show the validity of the model (I) by demonstrating that localized spatial patterns of object induced modulations in the electric field (electric images) are comparable to experimentally mapped 2-dimensional electric images and (II) by replicating earlier key findings showing that a normalized metric of electric image width provides an unambiguous cue for distance estimation. We then show that electric images and the distance metric vary systematically when an object is moved along the trunk. These potential ambiguities with regard to localization lead us to a spatiotemporal analysis of electric images. We introduce a new temporal metric for distance estimation that is based on the normalized spatial properties of electrical images. Finally, based on a survey of exploratory behavior, we show how objects situated at the tail, a region previously neglected, cast global electric images that extend over the whole sensory epithelium of the animals. Copyright © 2012 Elsevier Ltd. All rights reserved.

Global trade in ornamental fish from an Australian perspective: the case for revised import risk analysis and management strategies.

PubMed

Whittington, R J; Chong, R

2007-09-14

Over 1 billion ornamental fish comprising more than 4000 freshwater and 1400 marine species are traded internationally each year, with 8-10 million imported into Australia alone. Compared to other commodities, the pathogens and disease translocation risks associated with this pattern of trade have been poorly documented. The aim of this study was to conduct an appraisal of the effectiveness of risk analysis and quarantine controls as they are applied according to the Sanitary and Phytosanitary (SPS) agreement in Australia. Ornamental fish originate from about 100 countries and hazards are mostly unknown; since 2000 there have been 16-fold fewer scientific publications on ornamental fish disease compared to farmed fish disease, and 470 fewer compared to disease in terrestrial species (cattle). The import quarantine policies of a range of countries were reviewed and classified as stringent or non-stringent based on the levels of pre-border and border controls. Australia has a stringent policy which includes pre-border health certification and a mandatory quarantine period at border of 1-3 weeks in registered quarantine premises supervised by government quarantine staff. Despite these measures there have been many disease incursions as well as establishment of significant exotic viral, bacterial, fungal, protozoal and metazoan pathogens from ornamental fish in farmed native Australian fish and free-living introduced species. Recent examples include Megalocytivirus and Aeromonas salmonicida atypical strain. In 2006, there were 22 species of alien ornamental fish with established breeding populations in waterways in Australia and freshwater plants and molluscs have also been introduced, proving a direct transmission pathway for establishment of pathogens in native fish species. Australia's stringent quarantine policies for imported ornamental fish are based on import risk analysis under the SPS agreement but have not provided an acceptable level of protection (ALOP) consistent with government objectives to prevent introduction of pests and diseases, promote development of future aquaculture industries or maintain biodiversity. It is concluded that the risk analysis process described by the Office International des Epizooties under the SPS agreement cannot be used in a meaningful way for current patterns of ornamental fish trade. Transboundary disease incursions will continue and exotic pathogens will become established in new regions as a result of the ornamental fish trade, and this will be an international phenomenon. Ornamental fish represent a special case in live animal trade where OIE guidelines for risk analysis need to be revised. Alternatively, for countries such as Australia with implied very high ALOP, the number of species traded and the number of sources permitted need to be dramatically reduced to facilitate hazard identification, risk assessment and import quarantine controls.

Technical Note: Detection of gas bubble leakage via correlation of water column multibeam images

NASA Astrophysics Data System (ADS)

Schneider von Deimling, J.; Papenberg, C.

2011-07-01

Hydroacoustic detection of natural gas release from the seafloor has been conducted in the past by using singlebeam echosounders. In contrast modern multibeam swath mapping systems allow much wider coverage, higher resolution, and offer 3-D spatial correlation. However, up to the present, the extremely high data rate hampers water column backscatter investigations. More sophisticated visualization and processing techniques for water column backscatter analysis are still under development. We here present such water column backscattering data gathered with a 50 kHz prototype multibeam system. Water column backscattering data is presented in videoframes grabbed over 75 s and a "re-sorted" singlebeam presentation. Thus individual gas bubbles rising from the 24 m deep seafloor clearly emerge in the acoustic images and rise velocities can be determined. A sophisticated processing scheme is introduced to identify those rising gas bubbles in the hydroacoustic data. It applies a cross-correlation technique similar to that used in Particle Imaging Velocimetry (PIV) to the acoustic backscatter images. Tempo-spatial drift patterns of the bubbles are assessed and match very well measured and theoretical rise patterns. The application of this processing scheme to our field data gives impressive results with respect to unambiguous bubble detection and remote bubble rise velocimetry. The method can identify and exclude the main driver for misinterpretations, i.e. fish-mediated echoes. Even though image-based cross-correlation techniques are well known in the field of fluid mechanics for high resolution and non-inversive current flow field analysis, this technique was never applied in the proposed sense for an acoustic bubble detector.

Ocean Observation Instrument

NASA Technical Reports Server (NTRS)

1993-01-01

The Airborne Ocean Color Imager (AOCI) was developed by Daedalus Enterprises, Inc. for Ames Research Center under a Small Business Innovation Research (SBIR) contract as a simulator for an advanced oceanographic satellite instrument. The instrument measures water temperature and detects water color in nine wavelengths. Water color indicates chlorophyll content or phytoplankton. After EOCAP assistance and technical improvements, the AOCI was successfully commercialized by Daedalus Enterprises, Inc. One version provides commercial fishing fleets with information about fish locations, and the other is used for oceanographic research.

Diagnostic and Prognostic Utility of Fluorescence In situ Hybridization (FISH) Analysis in Acute Myeloid Leukemia.

PubMed

Gonzales, Patrick R; Mikhail, Fady M

2017-12-01

Acute myeloid leukemia (AML) is a hematologic neoplasia consisting of incompletely differentiated hematopoietic cells of the myeloid lineage that proliferate in the bone marrow, blood, and/or other tissues. Clinical implementation of fluorescence in situ hybridization (FISH) in cytogenetic laboratories allows for high-resolution analysis of recurrent structural chromosomal rearrangements specific to AML, especially in AML with normal karyotypes, which comprises approximately 33-50% of AML-positive specimens. Here, we review the use of several FISH probe strategies in the diagnosis of AML. We also review the standards and guidelines currently in place for use by clinical cytogenetic laboratories in the evaluation of AML. Updated standards and guidelines from the WHO, ACMG, and NCCN have further defined clinically significant, recurring cytogenetic anomalies in AML that are detectable by FISH. FISH continues to be a powerful technique in the diagnosis of AML, with higher resolution than conventional cytogenetic analysis, rapid turnaround time, and a considerable diagnostic and prognostic utility.

Gelation and thermal characteristics of microwave extracted fish gelatin-natural gum composite gels.

PubMed

Binsi, P K; Nayak, Natasha; Sarkar, P C; Joshy, C G; Ninan, George; Ravishankar, C N

2017-02-01

In this study, the gelation and thermal characteristics of microwave extracted fish scale gelatin blended with natural gums such as gum arabic (AG), xanthan gum (XG), guar gum (GG), and tragacanth gum (TG) was evaluated. The nature of interaction and behavior of gelatin in presence of various gums was confirmed by particle size analysis, viscosity profile, FT-IR analysis and turbidity measurements. DSC data revealed that addition of AG, TG and GG remarkably improved the thermal stability of fish gelatin gel. The composite gels of TG, AG, and XG exhibited higher hardness and bloom strength values as compared to pure fish gelatin implying its textural synergy. Based on qualitative descriptive analysis, TG was found to be superior in improving the stability of fish gelatin gel, closely followed by AG. The results suggest that addition of these gums can reduce syneresis and retard melting of gelatin gels at ambient temperature, which are otherwise soft and thermally unstable.

Differentiation of fresh and frozen-thawed fish samples using Raman spectroscopy coupled with chemometric analysis.

PubMed

Velioğlu, Hasan Murat; Temiz, Havva Tümay; Boyaci, Ismail Hakki

2015-04-01

The potential of Raman spectroscopy was investigated in terms of its capability to discriminate the species of the fish samples and determine their freshness according to the number of freezing/thawing cycles they exposed. Species discrimination analysis was carried out on sixty-four fish samples from six different species, namely horse mackerel (Trachurus trachurus), European anchovy (Engraulis encrasicolus), red mullet (Mullus surmuletus), Bluefish (Pomatamus saltatrix), Atlantic salmon (Salmo salar) and flying gurnard (Trigla lucerna). Afterwards, fish samples were exposed to different numbers of freezing/thawing cycles and separated into three batches, namely (i) fresh, (ii) once frozen-thawed (OF) and (iii) twice frozen-thawed (TF) samples, in order to perform the freshness analysis. Raman data collected were used as inputs for chemometric analysis, which enabled us to develop two main PCA models to successfully terminate the studies for both species discrimination and freshness determination analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Automated Segmentation of Light-Sheet Fluorescent Imaging to Characterize Experimental Doxorubicin-Induced Cardiac Injury and Repair.

PubMed

Packard, René R Sevag; Baek, Kyung In; Beebe, Tyler; Jen, Nelson; Ding, Yichen; Shi, Feng; Fei, Peng; Kang, Bong Jin; Chen, Po-Heng; Gau, Jonathan; Chen, Michael; Tang, Jonathan Y; Shih, Yu-Huan; Ding, Yonghe; Li, Debiao; Xu, Xiaolei; Hsiai, Tzung K

2017-08-17

This study sought to develop an automated segmentation approach based on histogram analysis of raw axial images acquired by light-sheet fluorescent imaging (LSFI) to establish rapid reconstruction of the 3-D zebrafish cardiac architecture in response to doxorubicin-induced injury and repair. Input images underwent a 4-step automated image segmentation process consisting of stationary noise removal, histogram equalization, adaptive thresholding, and image fusion followed by 3-D reconstruction. We applied this method to 3-month old zebrafish injected intraperitoneally with doxorubicin followed by LSFI at 3, 30, and 60 days post-injection. We observed an initial decrease in myocardial and endocardial cavity volumes at day 3, followed by ventricular remodeling at day 30, and recovery at day 60 (P < 0.05, n = 7-19). Doxorubicin-injected fish developed ventricular diastolic dysfunction and worsening global cardiac function evidenced by elevated E/A ratios and myocardial performance indexes quantified by pulsed-wave Doppler ultrasound at day 30, followed by normalization at day 60 (P < 0.05, n = 9-20). Treatment with the γ-secretase inhibitor, DAPT, to inhibit cleavage and release of Notch Intracellular Domain (NICD) blocked cardiac architectural regeneration and restoration of ventricular function at day 60 (P < 0.05, n = 6-14). Our approach provides a high-throughput model with translational implications for drug discovery and genetic modifiers of chemotherapy-induced cardiomyopathy.

Do scientists and fishermen collect the same size fish? Possible implications for exposure assessment.

PubMed

Burger, Joanna; Gochfeld, Michael; Burke, Sean; Jeitner, Christian W; Jewett, Stephen; Snigaroff, Daniel; Snigaroff, Ronald; Stamm, Tim; Harper, Shawn; Hoberg, Max; Chenelot, Heloise; Patrick, Robert; Volz, Conrad D; Weston, James

2006-05-01

Recreational and subsistence fishing plays a major role in the lives of many people, although most Americans obtain their fish from supermarkets or other commercial sources. Fish consumption has generally increased in recent years, largely because of the nutritional benefits. Recent concerns about contaminants in fish have prompted federal and state agencies to analyze fish (especially freshwater fish targeted by recreational anglers) for contaminants, such as mercury and polychlorinated biphenyls (PCBs), and to issue fish consumption advisories to help reduce the public health risks, where warranted. Scientists engaged in environmental sampling collect fish by a variety of means, and analyze the contaminants in those fish. Risk assessors use these levels as the basis for their advisories. Two assumptions of this methodology are that scientists collect the same size (and types) of fish that fishermen catch, and that, for some contaminants (such as methylmercury and PCBs), levels increase with the size and age of the fish. While many studies demonstrate a positive relationship between size and mercury levels in a wide range of different species of fish, the assumption that scientists collect the same size fish as fishermen has not been examined. The assumption that scientists collect the same size fish as those caught (and eaten) by recreationalists or subsistence fishermen is extremely important because contaminant levels are different in different size fish. In this article, we test the null hypothesis that there are no differences in the sizes of fish collected by Aleut fishermen, scientists (including divers), and commercial trawlers in the Bering Sea from Adak to Kiska. Aleut fishermen caught fish using rod-and-reel (fishing rods, hook, and fresh bait) from boats, as they would in their Aleutian villages. The scientists collected fish using rod-and-reel, as well as by scuba divers using spears up to 90 ft depths. A fisheries biologist collected fish from a research/commercial trawler operated under charter to the National Oceanographic and Atmospheric Administration (NOAA). The fish selected for sampling, including those caught commercially in the Bering Sea, represented different trophic levels, and are species regularly caught by Aleuts while fishing near their villages. Not all fish were caught by all three groups. There were no significant differences in length and weight for five species of fish caught by Aleuts, scientists, and fisheries trawls, and for an additional 3 species caught only by the Aleut and scientist teams. There were small, but significant, differences in the sizes of rock greenling (Hexagrammos lagocephalus) and red Irish lord (Hemilepidotus hemilepidotus) caught by the scientist and Aleut fishermen. No scientists caught rock greenling using poles; those speared by the divers were significantly smaller than those caught by the Aleuts. Further, there were no differences in the percent of males in the samples as a function of fishing method or type of fishermen, except for rockfish and red Irish lord. These data suggest that if scientists collect fish in the same manner as subsistence fishermen (in this case, using fishing rods from boats), they can collect the same-sized fish. The implications for exposure and risk assessment are that scientists should either engage subsistence and recreational fishermen to collect fish for analysis, or mimic their fishing methods to ensure that the fish collected are similar in size and weight to those being caught and consumed by these groups. Further, total length, standard length, and weight were highly correlated for all species of fish, suggesting that risk assessors could rely on recreational and commercial fishermen to measure total lengths for the purpose of correlating mercury levels with known size/mercury level relationships. Our data generally demonstrate that the scientists and trawlers can collect the same size fish as those caught by Aleuts, making contaminant analysis, and subsequent contaminant analysis, representative of the risks to fish consumers.

Sperm Scoring Using Multi-Spectral Flow Imaging and FISH-IS Final Report CRADA No. TC02088.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marchetti, F.; Morrissey, P. J.

This was to be a collaborative effort between The Regents of the University of California, Lawrence Livermore National Laboratory (LLNL) and Amnis Corporation, to develop an automated system for scoring sperm interphase cells for the presence of chromosomal abnormalities using fluorescence in situ hybridization and the Amnis ImageStream technology platform.

77 FR 67624 - Fisheries of the Northeastern United States; Atlantic Herring Fishery; Adjustment to 2013 Annual...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-13

...). Attachments to electronic comments will be accepted in Microsoft Word or Excel, WordPerfect, or Adobe PDF... accuracy against the scanned image of the paper VTRs submitted by the owner/ operator of the vessel. VTR... combination of recent fishing activity and a review of the scanned images of the original VTR were used to...

Return Spawning/Rearing Habitat to Anadromous/Resident Fish within the Fishing Creek to Legendary Bear Creek Analysis Area Watersheds; 2002-2003 Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Jr., Emmit E.

2004-03-01

This project is a critical component of currently on-going watershed restoration effort in the Lochsa River Drainage, including the Fishing (Squaw) Creek to Legendary Bear (Papoose) Creek Watersheds Analysis Area. In addition, funding for this project allowed expansion of the project into Pete King Creek and Cabin Creek. The goal of this project is working towards the re-establishment of healthy self-sustaining populations of key fisheries species (spring Chinook salmon, steelhead, bull trout, and westslope cutthroat trout) through returning historic habitat in all life stages (spawning, rearing, migration, and over-wintering). This was accomplished by replacing fish barrier road crossing culverts withmore » structures that pass fish and accommodate site conditions.« less

The antiviral defense mechanisms in mandarin fish induced by DNA vaccination against a rhabdovirus.

PubMed

Chen, Zhong-Yuan; Lei, Xiao-Ying; Zhang, Qi-Ya

2012-06-15

Plasmid DNAs containing Siniperca chuatsi rhabdovirus (SCRV) glycoprotein gene (pcDNA-G) and nucleoprotein gene (pcDNA-N) were constructed, and used to determine the antiviral immune response elicited by DNA vaccination in mandarin fish. In vitro and in vivo expression of the plasmid constructs was confirmed in transfected cells and muscle tissues of vaccinated fish by Western blot, indirect immunofluorescence or RT-PCR analysis. Fish injected with pcDNA-G exhibited protective effect against SCRV challenge with a relative percent survival (RPS) of 77.5%, but no significant protection (RPS of 2.5%) was observed in fish vaccinated with pcDNA-N. Immunohistochemical analysis showed that vaccination with pcDNA-G decreased histological lesions and suppressed the virus replication in fish target organs, e.g. kidney, liver, spleen, gill and heart. Transcriptional analysis further revealed that the expression levels of type I IFN system genes including interferon regulation factor-7 (IRF-7) gene, myxovirus resistance (Mx) gene and virus inhibitory protein (Viperin) gene were strongly up-regulated after injection with pcDNA-G, whereas the level of transcription of immunoglobulin M (IgM) gene did not show a statistically significant change. These results reveal that type I IFN antiviral immune response is rapidly triggered by the plasmid DNA containing rhabdovirus glycoprotein gene in fish, which offers an explanation of molecular mechanisms for DNA vaccination inducing mandarin fish resist to SCRV disease. Copyright © 2011 Elsevier B.V. All rights reserved.

Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

PubMed

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-05-19

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The campaign to DNA barcode all fishes, FISH-BOL.

PubMed

Ward, R D; Hanner, R; Hebert, P D N

2009-02-01

FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.

Mercury, Polychlorinated Biphenyls, Selenium, and Fatty Acids in Tribal Fish Harvests of the Upper Great Lakes.

PubMed

Dellinger, Matthew J; Olson, Jared T; Holub, Bruce J; Ripley, Michael P

2018-05-11

The Chippewa Ottawa Resource Authority monitors fish contaminants in Anishinaabe (Great Lake Native American) tribal fisheries. This article updates previously reported trends in two persistent bioaccumulative toxic (PBT) substances that are the primary contributors to consumption advisory limits for these fish: methylmercury (MeHg) and polychlorinated biphenyls (PCBs). Also, we report, for the first time, an analysis of nutritional benefit bioindicators and metrics in these same Upper Great Lakes fish harvests: selenium (Se) and omega-3 fatty acids (PUFA-3s). A novel risk/benefit quantification originally presented by Ginsberg et al. is reported here to characterize the tradeoffs between fatty acid benefits and toxic MeHg health outcomes. We also report a Se benefit metric to characterize the possible protective value against MeHg neurotoxicity based on Ralston et al. Congruent with Anishinaabe cultural motivations to consume fish from their ancestral fisheries, nutritional content was high in locally caught fish and, in some respects, superior to farmed/store-bought fish. These Great Lakes fish still contained levels of PBTs that require careful education and guidance for consumers. However, the contaminant trends suggest that these fish need not be abandoned as important (both culturally and nutritionally) food sources for the Anishinaabe who harvested them. © 2018 Society for Risk Analysis.

Fish or n3-PUFA intake and body composition: a systematic review and meta-analysis.

PubMed

Bender, N; Portmann, M; Heg, Z; Hofmann, K; Zwahlen, M; Egger, M

2014-08-01

Obesity is a major public health issue and an important contributor to the global burden of chronic disease and disability. Studies indicate that fish and omega-3 polyunsaturated fatty acids (n3-PUFA) supplements may help prevent cardiovascular and metabolic diseases. However, the effect of fish oil on body composition is still uncertain, so we performed a systematic review of randomized controlled trials and the first meta-analysis on the association between fish or fish oil intake and body composition measures. We found evidence that participants taking fish or fish oil lost 0.59 kg more body weight than controls (95% confidence interval [CI]: -0.96 to -0.21). Treatment groups lost 0.24 kg m(-2) (body mass index) more than controls (-0.40 to -0.08), and 0.49 % more body fat than controls (-0.97 to -0.01). Fish or fish oil reduced waist circumference by 0.81 cm (-1.34 to -0.28) compared with control. There was no difference for fat mass and lean body mass. Further research is needed to confirm or refute our findings and to reveal possible mechanisms by which n3-PUFAs might reduce weight. © 2014 The Authors. obesity reviews © 2014 World Obesity.

The effects of mariculture on heavy metal distribution in sediments and cultured fish around the Pearl River Delta region, south China.

PubMed

Liang, Peng; Wu, Sheng-Chun; Zhang, Jin; Cao, Yucheng; Yu, Shen; Wong, Ming-Hung

2016-04-01

Thirty-six sediment samples were collected from six mariculture sites and corresponding reference sites (approximately 200-300 m away from each mariculture site) to study the effects of mariculture on heavy metal: copper (Cu), zinc (Zn), chromium (Cr) and lead (Pb) distribution in sediments and cultured fish around the Pearl River Delta region, south China. The mean concentrations of Cu, Zn, Cr and Pb in all mariculture sediment samples were 109, 273, 99 and 33 mg/kg, compared with 63, 209, 56 and 23 mg/kg for reference sediment samples, respectively. The Pollution Load Index of sediment for each site was over 1, implying substantial heavy metal pollution. The results of principal component analysis and hierarchical clustering analysis indicate that marine aquaculture activities have enriched the surface sediments underneath mariculture rafts with Cu, Zn and Pb, possibly due to the accumulation of unconsumed fish feeds, fish excreta and antifouling paints (except Cr). Two kinds of fish feeds, feed pellets and trash fish commonly used in Hong Kong were analyzed. The concentrations of Zn and Cu contained in feed pellets were significantly higher (p < 0.05) than in trash fish due to addition of these elements as growth promoters during pellet production. However, the Pb content in trash fish (due to contamination) was significantly higher (p < 0.05) than in feed pellets. Three cultured fish species, namely red snapper (Lutjanus campechanus), orange-spotted grouper (Epinephelus coioides) and snubnose pompano (Trachinotus blochii), were collected from each mariculture site for metal analysis. Lead concentrations in 21 fish samples exceeded the Chinese safety guideline (0.5 mg/kg, GB18406.4-2001), indicating that Pb contamination in cultured fish would be a public health concern. Copyright © 2015. Published by Elsevier Ltd.

Changes in fish diversity and community structure in the central and southern Yellow Sea from 2003 to 2015

NASA Astrophysics Data System (ADS)

Chen, Yunlong; Shan, Xiujuan; Jin, Xianshi; Johannessen, Arne; Yang, Tao; Dai, Fangqun

2017-07-01

The central and southern Yellow Sea is an important overwintering ground for many fish species in the Bohai Sea and Yellow Sea. For better understanding the status of the fish community after years of heavy exploitation, variations in fish community structure and diversity were analyzed using data from bottom trawls during 2003-2015. Five fish assemblage indices all showed fluctuations without clear trends from 2003 to 2015, yet there were strong positive and significant correlations (P < 0.05) among them. The top-five dominant species accounted for a high weight percentage (49.7%-82.1%) in the annual fish catch. Multivariate analysis showed that two year groups could be pooled for the fish community: Group I consisted of the years 2006, 2007, 2008 and 2015, while Group II consisted of the years 2003, 2004, 2005, 2009, 2010 and 2014; the groups aggregated with 63.71% similarity, indicating a high level of similarity among all years. The multivariate dispersion values were 1.455 and 0.818 for Groups I and II, respectively, indicating greater variances in fish assemblage structure in Group I than that in Group II. Similarity of percentage analysis demonstrated that the average similarities for Group I and Group II were 71.58% and 67.51%, respectively. Size-spectra analysis revealed no consistent trend in the intercept and slope (P > 0.05); there were also no significant differences between the slope of the size-spectra and fishing effort. The catch per unit effort and mean individual weight analyses of the whole fish assemblage both showed a significantly decreasing trend over time. Overall, the results showed that the fish community structure in the central and southern Yellow Sea was relatively stable from 2003 to 2015 and the study could be used as a reference for supporting ecosystem-based fishery management.

Fishing decisions under uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrison, C.G.

1982-02-01

The drilling manager often is forced by an extended fishing operation to choose between the known costs incurred with abandonment of retrieval attempts and the unknown costs of continuing fishing operations. The successful manager makes the decision that costs the company the least money. Continuing fishing operations beyond some economic limit is failure, even if the fish is retrieved and that portion of the hole saved, because more money has been spent in the fishing attempt than would have been spent by not fishing. The strategy is to minimize losses. This analysis closely follows the theory of utility developed bymore » J. von Neuman and O. Morgenstern. 1 ref.« less

Shifts in stable-isotope signatures confirm parasitic relationship of freshwater mussel glochidia attached to host fish

USGS Publications Warehouse

Fritts, Mark W.; Fritts, Andrea K.; Carleton, Scott A.; Bringolf, Robert B.

2013-01-01

The parasitic nature of the association between glochidia of unionoidean bivalves and their host fish (i.e. the role of fish hosts in providing nutritional resources to the developing glochidia) is still uncertain. While previous work has provided descriptions of development of glochidia on fish hosts, earlier studies have not explicitly documented the flow of nutrition from the host fish to the juvenile mussel. Therefore, our objective was to use stable isotope analysis to quantitatively document nutrient flow between fish and glochidia. Glochidia were collected from nine adult Lampsilis cardium and used to inoculate Micropterus salmoides(n = 27; three fish per maternal mussel) that produced juvenile mussels for the experiment. Adult mussel tissue samples, glochidia, transformed juvenile mussels and fish gill tissues were analysed for δ15N and δ13C isotope ratios. We used a linear mixing model to estimate the fraction of juvenile mussel tissue derived from the host fish's tissue during attachment. Our analyses indicate a distinct shift in both C and N isotopic ratios from the glochidial stage to the juvenile stage during mussel attachment and development. Linear mixing model analysis indicated that 57.4% of the δ15N in juvenile tissues were obtained from the host fish. This work provides novel evidence that larval unionoideans are true parasites that derive nutrition from host fish during their metamorphosis into the juvenile stage.

Accumulation and distribution of copper and zinc in both water and some vital tissues of two fish species (Tilapia zillii and Mugil cephalus) of Lake Qarun, Fayoum Province, Egypt.

PubMed

Authman, Mohammad M N; Abbas, Hossam H H

2007-07-01

This study was carried out on Lake Qarun, Fayoum Province, Egypt throughout four seasons, spring 2004 to winter 2005. The concentration of Zn in water as well as in fish organs was always higher than Cu. Correlations between concentration of heavy metals in water and fish organs were elucidated. The concentrations of heavy metals in fish samples indicated that Tilapia zillii were higher than those of Mugil cephalus, which is attributed to their feeding behavior. It was found that these metals have been accumulated in fish organs in different concentrations, which were much higher, several times in some cases, than those found in the surrounding water. The analysis of variance (ANOVA, 1-way analysis) for heavy metals in water and fish organs indicated significant difference. Bioaccumulation factor values showed that the trend of accumulation of metals in fish organs was apparent in liver, gills and muscle, respectively. Lesions deformations were detected and analyzed to clarify the possible role of water pollution on the efficiency of fish and hence the declining fish production of Lake Qarun. The results suggest that the Lake Qarun system is contaminated with heavy metals and the consumption of fishes of the Lake could pose health damage to the local population whose diet consists mainly of fish. A recommendation is given to rescue Lake Qarun from these serious ecological problems.

Hidden chromosome 8 abnormalities detected by FISH in adult primary myelodysplastic syndromes.

PubMed

Panani, Anna D; Pappa, Vasiliki

2005-01-01

Acquired clonal chromosomal abnormalities are found in about 30-50% of primary myelodysplastic syndromes (MDS). These abnormalities are predominantly characterized by total/partial chromosomal losses or gains and rarely by balanced structural aberrations. Trisomy 8 represents the most common chromosomal gain. In the present study, the numerical aberration of chromosome 8 was evaluated by the fluorescence in situ hybridization (FISH) technique in MDS, and the results compared with those of conventional cytogenetics. Thirty adult patients with primary MDS, 17 with a normal karyotype and 13 with several chromosomal abnormalities except chromosome 8, were included in this study. On comparing the results of FISH and conventional cytogenetics, a superiority of FISH over the karyotype was detected in 3 cases. In one of them, further cytogenetic analysis confirmed the FISH results. Nevertheless, the FISH technique has limitations, detecting only abnormalities specific for the target FISH probe used In clinical practice, conventional cytogenetics continues to be the basic technique for MDS patient evaluation. However, a large number of metaphases, even those of poor quality, must be analyzed in each case. The FISH technique could be considered to be complementary to achieve a more accurate analysis.

Evolutionary analysis of the jacalin-related lectin family genes in 11 fishes.

PubMed

Cao, Jun; Lv, Yueqing

2016-09-01

Jacalin-related lectins are a type of carbohydrate-binding proteins, which are distributed across a wide variety of organisms and involved in some important biological processes. The evolution of this gene family in fishes is unknown. Here, 47 putative jacalin genes in 11 fish species were identified and divided into 4 groups through phylogenetic analysis. Conserved gene organization and motif distribution existed in each group, suggesting their functional conservation. Some fishes have eleven jacalin genes, while others have only one or zero gene in their genomes, suggesting dynamic changes in the number of jacalin genes during the evolution of fishes. Intragenic recombination played a key role in the evolution of jacalin genes. Synteny analyses of jacalin genes in some fishes implied conserved and dynamic evolution characteristics of this gene family and related genome segments. Moreover, a few functional divergence sites were identified within each group pairs. Divergent expression profiles of the zebra fish jacalin genes were further investigated in different stresses. The results provided a foundation for exploring the characterization of the jacalin genes in fishes and will offer insights for additional functional studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Migratory delay leads to reduced passage success of Atlantic salmon smolts at a hydroelectric dam

USGS Publications Warehouse

Nyqvist, Daniel; Greenberg, L.; Goerig, E.; Calles, O.; Bergman, E.; Ardren, William R.; Castro-Santos, Theodore R.

2017-01-01

Passage of fish through hydropower dams is associated with mortality, delay, increased energy expenditure and migratory failure for migrating fish and the need for remedial measures for both upstream and downstream migration is widely recognised. A functional fish passage must ensure safe and timely passage routes that a substantial portion of migrating fish will use. Passage solutions must address not only the number or percentage of fish that successfully pass a barrier, but also the time it takes to pass. Here, we used radiotelemetry to study the functionality of a fish bypass for downstream-migrating wild-caught and hatchery-released Atlantic salmon smolts. We used time-to-event analysis to model the influence of fish characteristics and environmental variables on the rates of a series of events associated with dam passage. Among the modelled events were approach rate to the bypass entry zone, retention rates in both the forebay and the entry zone and passage rates. Despite repeated attempts, only 65% of the tagged fish present in the forebay passed the dam. Fish passed via the bypass (33%), via spill (18%) and via turbines (15%). Discharge was positively related to approach, passage and retention rates. We did not detect any differences between wild and hatchery fish. Even though individual fish visited the forebay and the entry zone on multiple occasions, most fish passed during the first exposures to these zones. This study underscores the importance of timeliness to passage success and the usefulness of time-to-event analysis for understanding factors governing passage performance.

Proteomic Analysis of Cytoskeleton Proteins in Fish.

PubMed

Gotesman, Michael; Menanteau-Ledouble, Simon; El-Matbouli, Mansour

2016-01-01

In this chapter, we describe laboratory protocols for rearing fish and a simple and efficient method of extracting and identifying pathogen and host proteins that may be involved in entry and replication of commercially important fish viruses. We have used the common carp (Cyprinus carpio L.) and goldfish (Cyprinus auratus) as a model system for studies of proteins involved in viral entry and replication. The chapter describes detailed protocols for maintenance of carp, cell culture, antibody purification of proteins, and use of electrospray-ionization mass spectrometry analysis to screen and identify cytoskeleton and other proteins that may be involved in viral infection and propagation in fish.

Fish consumption and depressive symptoms in undergraduate students: A cross-sectional analysis.

PubMed

Hamazaki, K; Natori, T; Kurihara, S; Murata, N; Cui, Z-G; Kigawa, M; Morozumi, R; Inadera, H

2015-11-01

Emerging evidence suggests that fish consumption may have beneficial effects on mood disorders. However, no study has been reported on this issue in young adults to date. The aim of this study was to investigate the relationship between fish consumption and depressive symptoms in Japanese undergraduate students. The 20-item Center for Epidemiologic Studies Depression Scale was used to measure depressive symptoms with a cut-off score of 16. A total of 4190 completed questionnaires (from 2124 men and 2066 women) were received for analysis. Multivariate logistic analysis showed that fish intake was inversely associated with risk of depressive symptoms in undergraduate students. After adjustment for possible confounders, the odds-ratios (95% confidence intervals) for fish intake 1-2 times/month, 1-2 times/week, 3-4 times/week, and almost every day (compared with "almost never") were 0.78 (0.62-0.99), 0.70 (0.56-0.87), 0.67 (0.53-0.85) and 0.65 (0.46-0.92), respectively. This association tended to be stronger in women than in men. Frequent fish consumption in undergraduate students seems to moderate depressive symptoms. Further research is warranted to clarify the causality. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Mitochondrial cytochrome b DNA sequence variations: an approach to fish species identification in processed fish products.

PubMed

Pepe, Tiziana; Trotta, Michele; di Marco, Isolina; Cennamo, Paola; Anastasio, Aniello; Cortesi, Maria Luisa

2005-02-01

The identification of fish species in food products is problematic because morphological features of the fish are partially or completely lost during processing. It is important to determine fish origin because of the increasing international seafood trade and because European Community Regulation 104/2000 requires that the products be labeled correctly. Sequence analysis of PCR products from a conserved region of the cytochrome b gene was used to identity fish species belonging to the families Gadidae and Merluccidae in 18 different processed fish products. This method allowed the identification of fish species in all samples. Fish in all of the examined products belonged to these two families, with the exception of one sample of smoked baccalà (salt cod), which was not included in the Gadidae cluster.

Tilapia fish microbial spoilage monitored by a single optical gas sensor.

PubMed

Semeano, Ana T S; Maffei, Daniele F; Palma, Susana; Li, Rosamaria W C; Franco, Bernadette D G M; Roque, Ana C A; Gruber, Jonas

2018-07-01

As consumption of fish and fish-based foods increases, non-destructive monitoring of fish freshness also becomes more prominent. Fish products are very perishable and prone to microbiological growth, not always easily detected by organoleptic evaluation. The analysis of the headspace of fish specimens through gas sensing is an interesting approach to monitor fish freshness. Here we report a gas sensing method for monitoring Tilapia fish spoilage based on the application of a single gas sensitive gel material coupled to an optical electronic nose. The optical signals of the sensor and the extent of bacterial growth were followed over time, and results indicated good correlation between the two determinations, which suggests the potential application of this simple and low cost system for Tilapia fish freshness monitoring.

Imaging of Jurassic fossils from the Talbragar Fish Bed using fluorescence, photoluminescence, and elemental and mineralogical mapping.

PubMed

Frese, Michael; Gloy, Gerda; Oberprieler, Rolf G; Gore, Damian B

2017-01-01

The Talbragar Fish Bed is one of Australia's most important Jurassic deposits for freshwater fishes, land plants and aquatic and terrestrial insects. The site has yielded many well preserved fossils, which has led to the formal description of numerous new species and higher taxa. The excellent preservation of many fossils has allowed detailed anatomical studies, e.g. of the early teleost fish Cavenderichthys talbragarensis (Woodward, 1895). Here we report on the fluorescent characteristics and mineral composition of a range of Talbragar fossils. Most specimens fluoresce under ultraviolet, blue and green light. Elemental and mineralogical analyses revealed that the Talbragar fossils consist predominantly of quartz (SiO2), a mineral that is likely to account for the observed fluorescence, with trace kaolinite (Al2Si2O5(OH)4) in some of the fish fossils. Rock matrices are predominantly composed of quartz and goethite (FeO(OH)). Closer inspection of a plant leaf (Pentoxylon australicum White, 1981) establishes fluorescence as a useful tool for the visualisation of anatomical details that are difficult to see under normal light conditions.

Imaging of Jurassic fossils from the Talbragar Fish Bed using fluorescence, photoluminescence, and elemental and mineralogical mapping

PubMed Central

Gloy, Gerda; Oberprieler, Rolf G.; Gore, Damian B.

2017-01-01

The Talbragar Fish Bed is one of Australia’s most important Jurassic deposits for freshwater fishes, land plants and aquatic and terrestrial insects. The site has yielded many well preserved fossils, which has led to the formal description of numerous new species and higher taxa. The excellent preservation of many fossils has allowed detailed anatomical studies, e.g. of the early teleost fish Cavenderichthys talbragarensis (Woodward, 1895). Here we report on the fluorescent characteristics and mineral composition of a range of Talbragar fossils. Most specimens fluoresce under ultraviolet, blue and green light. Elemental and mineralogical analyses revealed that the Talbragar fossils consist predominantly of quartz (SiO2), a mineral that is likely to account for the observed fluorescence, with trace kaolinite (Al2Si2O5(OH)4) in some of the fish fossils. Rock matrices are predominantly composed of quartz and goethite (FeO(OH)). Closer inspection of a plant leaf (Pentoxylon australicum White, 1981) establishes fluorescence as a useful tool for the visualisation of anatomical details that are difficult to see under normal light conditions. PMID:28582427

Aerial Jumping in the Trinidadian Guppy (Poecilia reticulata)

PubMed Central

Soares, Daphne; Bierman, Hilary S.

2013-01-01

Many fishes are able to jump out of the water and launch themselves into the air. Such behavior has been connected with prey capture, migration and predator avoidance. We found that jumping behavior of the guppy Poecilia reticulata is not associated with any of the above. The fish jump spontaneously, without being triggered by overt sensory cues, is not migratory and does not attempt to capture aerial food items. Here, we use high speed video imaging to analyze the kinematics of the jumping behavior P. reticulata. Fish jump from a still position by slowly backing up while using its pectoral fins, followed by strong body trusts which lead to launching into the air several body lengths. The liftoff phase of the jump is fast and fish will continue with whole body thrusts and tail beats, even when out of the water. This behavior occurs when fish are in a group or in isolation. Geography has had substantial effects on guppy evolution, with waterfalls reducing gene flow and constraining dispersal. We suggest that jumping has evolved in guppies as a behavioral phenotype for dispersal. PMID:23613883

Presence of a predator image in potential breeding sites and oviposition responses of a dengue vector.

PubMed

Dieng, Hamady; Satho, Tomomitsu; Suradi, Nur Farrahana Binti; Hakim, Hafijah; Abang, Fatimah; Aliasan, Nur Ezzati; Miake, Fumio; Zuharah, Wan Fatma; Kassim, Nur Faeza A; Majid, Abdul Hafiz A; Fadzly, Nik; Vargas, Ronald E Morales; Morales, Noppawan P; Noweg, Gabriel Tonga

2017-12-01

In dengue vector control, attempts to minimize or replace the use of pesticides have mostly involved use of predators, but success has been severely impeded by difficulties associated with financial and environmental costs, predator mass production, and persistence in target habitats. Visual deterrents have been used successfully to control animal pests, in some cases in an effort to replace pesticide use. Despite evidence that visual signals are crucial in site choice for egg deposition by dengue vectors, and that female mosquitoes respond to artificial predation, the role of predator intimidation as it affects the oviposition behavior of dengue vectors remains largely unexplored. Here, we examined the oviposition responses of Aedes aegypti exposed to various mosquito predator pictures. Gravid females were presented with equal opportunities to oviposit in two cups with predator images [Toxorhynchites splendens-TXI, Goldfish (Carassius auratus)-small (SFI) and large (LFI) and Tx. splendens+Goldfish-TXFI] and two others without pictures. Differences in egg deposition were examined between sites with and without these images. When given a chance to oviposit in cups with and without TXI, Ae. aegypti females were similarly attracted to both sites. When provided an opportunity to oviposit in cups displaying pictures of fish (SFI or LFI) and blank cups, egg deposition rates were much lower in the fish picture sites. Females showed a preference for blank cups over TXFI for egg deposition. They also equally avoided cups with pictures of fish, regardless of the size of the picture. Our results indicate that the presence of images of goldfish and their association with Tx. larvae significantly reduced egg deposition by Ae. aegypti, and this was not the case with the predatory larvae alone. The observations that the images of natural predators can repel gravid females of a dengue vector provide novel possibilities to develop effective and inexpensive alternative tools to harmful insecticides. Copyright © 2017 Elsevier B.V. All rights reserved.

Mind the gap: the minimal detectable separation distance between two objects during active electrolocation.

PubMed

Fechler, K; Holtkamp, D; Neusel, G; Sanguinetti-Scheck, J I; Budelli, R; von der Emde, G

2012-12-01

In a food-rewarded two-alternative forced-choice procedure, it was determined how well the weakly electric elephantnose fish Gnathonemus petersii can sense gaps between two objects, some of which were placed in front of complex backgrounds. The results show that at close distances, G. petersii is able to detect gaps between two small metal cubes (2 cm × 2 cm × 2 cm) down to a width of c. 1·5 mm. When larger objects (3 cm × 3 cm × 3 cm) were used, gaps with a width of 2-3 mm could still be detected. Discrimination performance was better (c. 1 mm gap size) when the objects were placed in front of a moving background consisting of plastic stripes or plant leaves, indicating that movement in the environment plays an important role for object identification. In addition, the smallest gap size that could be detected at increasing distances was determined. A linear relationship between object distance and gap size existed. Minimal detectable gap sizes increased from c. 1·5 mm at a distance of 1 cm, to 20 mm at a distance of 7 cm. Measurements and simulations of the electric stimuli occurring during gap detection revealed that the electric images of two close objects influence each other and superimpose. A large gap of 20 mm between two objects induced two clearly separated peaks in the electric image, while a 2 mm gap caused just a slight indentation in the image. Therefore, the fusion of electric images limits spatial resolution during active electrolocation. Relative movements either between the fish and the objects or between object and background might improve spatial resolution by accentuating the fine details of the electric images. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Optical tracking of embryonic vertebrates behavioural responses using automated time-resolved video-microscopy system

NASA Astrophysics Data System (ADS)

Walpitagama, Milanga; Kaslin, Jan; Nugegoda, Dayanthi; Wlodkowic, Donald

2016-12-01

The fish embryo toxicity (FET) biotest performed on embryos of zebrafish (Danio rerio) has gained significant popularity as a rapid and inexpensive alternative approach in chemical hazard and risk assessment. The FET was designed to evaluate acute toxicity on embryonic stages of fish exposed to the test chemical. The current standard, similar to most traditional methods for evaluating aquatic toxicity provides, however, little understanding of effects of environmentally relevant concentrations of chemical stressors. We postulate that significant environmental effects such as altered motor functions, physiological alterations reflected in heart rate, effects on development and reproduction can occur at sub-lethal concentrations well below than LC10. Behavioral studies can, therefore, provide a valuable integrative link between physiological and ecological effects. Despite the advantages of behavioral analysis development of behavioral toxicity, biotests is greatly hampered by the lack of dedicated laboratory automation, in particular, user-friendly and automated video microscopy systems. In this work we present a proof-of-concept development of an optical system capable of tracking embryonic vertebrates behavioral responses using automated and vastly miniaturized time-resolved video-microscopy. We have employed miniaturized CMOS cameras to perform high definition video recording and analysis of earliest vertebrate behavioral responses. The main objective was to develop a biocompatible embryo positioning structures that were suitable for high-throughput imaging as well as video capture and video analysis algorithms. This system should support the development of sub-lethal and behavioral markers for accelerated environmental monitoring.

ULTRASONOGRAPHIC DETECTION OF INGESTED FISHING LINES IN LOGGERHEADS ( CARETTA CARETTA).

PubMed

Franchini, Delia; Valastro, Carmela; Ciccarelli, Stefano; Caprio, Francesco; Lenoci, Diana; Di Bello, Antonio

2018-05-23

Loggerhead sea turtles ( Caretta caretta) are among the most frequent victims of bycatch in drifting longlines, and the ingestion of fish hooks and fishing lines is one of the most frequent causes of death of sea turtles. The aim of this study was to evaluate whether coelomic ultrasound (US) can be decisive, not only for diagnosis but also to optimize surgical planning based on preoperative evaluation of the bowel conditions and, in addition, to see if there are characteristic sonographic findings in sea turtles associated with the ingestion of fishing lines. Physical examination, hematology, blood chemistry, radiographs, and US examination were performed in 37 loggerhead sea turtles with suspected or known ingestion of fish hooks or monofilament fishing lines. During the ultrasonographic examinations, the loggerhead sea turtles were placed in dorsal recumbency and the prefemoral left and right acoustic windows were used. Nine wild loggerheads had sonographic findings of intestinal and coelomic abnormalities, and the sonographic images were compared with the surgical findings. Ultrasonography positively identified the foreign body in 89% (8/9) animals. The presence of intestinal plication (in all loggerhead turtles) and ultrasonographic visualization of the linear foreign body was always consistent with the ingestion of a fishing line. In sea turtles, fishing lines cause a corrugated appearance in the small intestine due to increased/unproductive peristalsis. The affected small bowel loops are usually dilated with fluid. In the present study, coelomic US allowed us to make a thorough evaluation of the characteristics, number, and severity of the bowel wall lesions in the animals, thus ensuring the planning of a correct surgical procedure. We suggest that US examination of the coelomic cavity should be complementary to radiographic survey in cases of suspected ingestion of fish hooks and fishing lines by sea turtles.

Impact of Monsoon to Aquatic Productivity and Fish Landing at Pesawaran Regency Waters

NASA Astrophysics Data System (ADS)

Kunarso; Zainuri, Muhammad; Ario, Raden; Munandar, Bayu; Prayogi, Harmon

2018-02-01

Monsoon variability influences the productivity processes in the ocean and has different responses in each waters. Furthermore, variability of marine productivity affects to the fisheries resources fluctuation. This research has conducted using descriptive method to investigate the consequences of monsoon variability to aquatic productivity, sea surface temperature (SST), fish catches, and fish season periods at Pesawaran Regency waters, Lampung. Variability of aquatic productivity was determined based on chlorophyll-a indicator from MODIS satellite images. Monsoon variability was governed based on wind parameters and fish catches from fish landing data of Pesawaran fish market. The result showed that monsoon variability had affected to aquatic productivity, SST, and fish catches at Pesawaran Regency waters. Maximum wind speed and lowest SST occurred twice in a year, December to March and August to October, which the peaks were on January (2.55 m/s of wind speed and 29.66°C of SST) and September (2.44 m/s of wind speed and 29.06°C of SST). Also, Maximum aquatic productivity happened on January to March and July to September, which it was arisen simultaneously with maximum wind speed and the peaks was 0.74 mg/m3 and 0.78 mg/m3, on February and August respectively. The data showed that fish catches decreased along with strong wind speed and low SST. However, when weak wind speed and high SST occurred, fish catches increased. The correlation between Catch per Unit Effort (CPUE) with SST, wind speed, and chlorophyll-a was at value 0.76, -0.67, and -0.70, respectively. The high rate fish catches in Pesawaran emerged on March-May and September-December.

Learning to swim, again: Axon regeneration in fish.

PubMed

Rasmussen, Jeffrey P; Sagasti, Alvaro

2017-01-01

Damage to the central nervous system (CNS) of fish can often be repaired to restore function, but in mammals recovery from CNS injuries usually fails due to a lack of axon regeneration. The relatively growth-permissive environment of the fish CNS may reflect both the absence of axon inhibitors found in the mammalian CNS and the presence of pro-regenerative environmental factors. Despite their different capacities for axon regeneration, many of the physiological processes, intrinsic molecular pathways, and cellular behaviors that control an axon's ability to regrow are conserved between fish and mammals. Fish models have thus been useful both for identifying factors differing between mammals and fish that may account for differences in CNS regeneration and for characterizing conserved intrinsic pathways that regulate axon regeneration in all vertebrates. The majority of adult axon regeneration studies have focused on the optic nerve or spinal axons of the teleosts goldfish and zebrafish, which have been productive models for identifying genes associated with axon regeneration, cellular mechanisms of circuit reestablishment, and the basis of functional recovery. Lampreys, which are jawless fish lacking myelin, have provided an opportunity to study regeneration of well defined spinal cord circuits. Newer larval zebrafish models offer numerous genetic tools and the ability to monitor the dynamic behaviors of extrinsic cell types regulating axon regeneration in live animals. Recent advances in imaging and gene editing methods are making fish models yet more powerful for investigating the cellular and molecular underpinnings of axon regeneration. Copyright © 2016 Elsevier Inc. All rights reserved.

The role of internal waves in larval fish interactions with potential predators and prey

NASA Astrophysics Data System (ADS)

Greer, Adam T.; Cowen, Robert K.; Guigand, Cedric M.; Hare, Jonathan A.; Tang, Dorothy

2014-09-01

Tidally driven internal wave packets in coastal environments have the potential to influence patchiness of larval fishes, prey, and gelatinous predators. We used the In Situ Ichthyoplankton Imaging System (ISIIS) to synoptically sample larval fishes, copepods, and planktonic predators (ctenophores, hydromedusae, chaetognaths, and polychaetes) across these predictable features in the summer near Stellwagen Bank, Massachusetts, USA. Full water column profiles and fixed depth transects (∼10 m depth) were used to quantify vertical and horizontal components of the fish and invertebrate distributions during stable and vertically mixed conditions associated with tidally generated internal waves. Larval fishes, consisting mostly of Urophycis spp., Merluccius bilinearis, and Labridae, were concentrated near the surface, with larger sizes generally occupying greater depths. During stable water column conditions, copepods formed a near surface thin layer several meters above the chlorophyll-a maximum that was absent when internal waves were propagating. In contrast, ctenophores and other predators were much more abundant at depth, but concentrations near 10 m increased immediately after the internal hydraulic jump mixed the water column. During the propagation of internal waves, the fine-scale abundance of larval fishes was more correlated with the abundance of gelatinous predators and less correlated with copepods compared to the stable conditions. Vertical oscillations caused by the internal hydraulic jump can disperse patches of zooplankton and force surface dwelling larval fishes into deeper water where probability of predator contact is increased, creating conditions potentially less favorable for larval fish growth and survival on short time scales.

Molecular Approach to the Identification of Fish in the South China Sea

PubMed Central

Zhang, Junbin; Hanner, Robert

2012-01-01

Background DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world's fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea. Methodology/Principal Findings DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species. Conclusions/Significance The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy. PMID:22363454

DNA barcode-based molecular identification system for fish species.

PubMed

Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

2010-12-01

In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

Morphological and molecular characterization of a marine fish trypanosome from South Africa, including its development in a leech vector.

PubMed

Hayes, Polly M; Lawton, Scott P; Smit, Nico J; Gibson, Wendy C; Davies, Angela J

2014-01-24

Trypanosomes are ubiquitous blood parasites of marine and freshwater fishes, typically transmitted by aquatic leeches. Phylogenetic studies have been dominated by examples derived from freshwater fishes, with few marine representatives. Furthermore, life cycle studies on marine fish trypanosomes have focused on those of the northern hemisphere. In this investigation, we have examined the life cycle and molecular taxonomy of a marine fish trypanosome from South Africa. To locate trypanosome stages, leeches were removed from fishes captured on the west and south coasts of South Africa, and fish blood films and leech squashes were Giemsa-stained and screened; leeches were also examined histologically. To determine whether trypanosome stages in fishes and leeches were of the same genotype, DNA was extracted from Giemsa-stained fish blood films and leech squashes, and from fish whole blood. Fragments of the 18S rRNA gene were amplified by PCR using trypanosome-specific primers and sequenced. Resulting sequence data were compared with each other and with published trypanosome 18S rDNA sequences, and used for phylogenetic analysis. Trypanosomes were detected in blood films from fishes of the families Clinidae, Blenniidae and Gobiidae. The flagellates ranged in size and staining properties within the films and across fish hosts. In squashes and histological sections of adult and juvenile leeches, identified as Zeylanicobdella arugamensis, trypanosome developmental stages were predominantly slender epimastigotes. Sequence data showed that trypanosomes derived from fishes were identical, irrespective of whether they were small or large forms; sequences derived largely from leech epimastigotes were also identical to those obtained from fish trypanosomes. Fish and leech trypanosome sequences fell into a marine fish aquatic clade, and aligned most closely with two trypanosome sequences from marine fishes off Norway. Combined morphological and molecular methods indicate that the trypanosomes examined here represent a single pleomorphic species, rather than the three species described originally. This species is identified as Trypanosoma nudigobii Fantham, 1919 with the leech Z. arugamensis as its vector, and T. capigobii Fantham, 1919 and T. blenniclini Fantham, 1930 are regarded as junior synonyms of the species. Phylogenetic analysis establishes its affinity with marine fish trypanosomes off Norway.

The importance of environmental quality and catch potential to fishing site selection by freshwater anglers in Mississippi

USGS Publications Warehouse

Schramm, H.L.; Gerard, P.D.; Gill, D.A.

2003-01-01

We measured the importance of 24 fishing site attributes to Mississippi freshwater anglers. Factor analysis identified four multiattribute factors as important in the selection of fishing location: CLEAN ENVIRONMENT CATCH, COST AND HARVEST and AMENITIES AND SAFETY. In general, the importance of site selection factors differed little among anglers grouped by preferred type of fish, preferred fishing location (lakes and reservoirs, rivers and streams, ponds, or reservoir tailwaters), usual manner of fishing (engine-powered boat, nonpowered boat, or shore), or change in fishing frequency. COST AND HARVEST was more important to anglers with high harvest orientations. We found low correlations between site selection factor importance scores and angler age, fishing frequency, fishing expenditures, or fishing motivation factors. We suggest that the general lack of differences in site selection factors among angler groups indicates that management strategies to improve fishing site attributes should benefit all angler groups. Clean fishing environments and awareness of the availability of desired sport fishes were "very" or "extremely" important to fishing site selection by more than 70% of Mississippi freshwater anglers and should be priority management objectives.

Unconstrained and Noninvasive Measurement of Swimming Behavior of Small Fish Based on Ventilatory Signals

NASA Astrophysics Data System (ADS)

Kitayama, Shigehisa; Soh, Zu; Hirano, Akira; Tsuji, Toshio; Takiguchi, Noboru; Ohtake, Hisao

Ventilatory signal is a kind of bioelectric signals reflecting the ventilatory conditions of fish, and has received recent attention as an indicator for assessment of water quality, since breathing is adjusted by the respiratory center according to changes in the underwater environment surrounding the fish. The signals are thus beginning to be used in bioassay systems for water examination. Other than ventilatory conditions, swimming behavior also contains important information for water examination. The conventional bioassay systems, however, only measure either ventilatory signals or swimming behavior. This paper proposes a new unconstrained and noninvasive measurement method that is capable of conducting ventilatory signal measurement and behavioral analysis of fish at the same time. The proposed method estimates the position and the velocity of a fish in free-swimming conditions using power spectrum distribution of measured ventilatory signals from multiple electrodes. This allowed the system to avoid using a camera system which requires light sources. In order to validate estimation accuracy, the position and the velocity estimated by the proposed method were compared to those obtained from video analysis. The results confirmed that the estimated error of the fish positions was within the size of fish, and the correlation coefficient between the velocities was 0.906. The proposed method thus not only can measure the ventilatory signals, but also performs behavioral analysis as accurate as using a video camera.

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

USGS Publications Warehouse

Luczkovich, J.J.; Ward, G.P.; Johnson, J.C.; Christian, R.R.; Baird, D.; Neckles, H.; Rizzo, W.M.

2002-01-01

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa. present in Hatodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity greater than or equal to 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers, and piscivores. These trophic groups, cross-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.

On inappropriately used neuronal circuits as a possible basis of the ``loop-swimming'' behaviour of fish under reduced gravity: a theoretical study

NASA Astrophysics Data System (ADS)

Anken, R. H.; Rahmann, H.

One hypothesis for the explanation of the so-called ``loop-swimming'' behaviour in fish when being subjected to reduced gravity assumes that the activities of the differently weighted otoliths of the two labyrinths are well compensated on ground but that a functional asymmetry is induced in weightlessness, resulting in a tonus asymmetry of the body and by this generating the ``loop-swimming'' behaviour. The basis of this abnormal behaviour has to be searched for in the central nervous system (cns), where the signal-transduction from the inner ear- related signal internalisation to the signal response takes place. Circuits within the CNS of fish, that could possibly generate the ``loop-swimming'', might be as follows: An asymmetric activation of vestibulospinal circuits would directly result in a tonus asymmetry of the body. An asymmetric activation of the oculomotor nucleus would generate an asymmetrical rotation of the eyes. This would cause in its turn asymmetric images on the two retinas, which were forwarded to the diencephalic accessory optic system (AOS). It is the task of the AOS to stabilize retinal images, thereby involving the cerebellum, which is the main integration center for sensory and motor modalities. With this, the cerebellar output would generate a tonus asymmetry of the body in order to make the body of the fish follow its eyes. Such movements (especially when assuming an open loop control) would end up in the aforementioned ``loop-swimming'' behaviour.

Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes

PubMed Central

Wang, Ying; Yang, Liandong; Zhou, Kun; Zhang, Yanping; Song, Zhaobin; He, Shunping

2015-01-01

Abstract Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes. PMID:26454018

Rapid analysis of malachite green and leucomalachite green in fish muscles with surface-enhanced resonance Raman scattering.

PubMed

Zhang, Yuanyuan; Yu, Wansong; Pei, Lu; Lai, Keqiang; Rasco, Barbara A; Huang, Yiqun

2015-02-15

Surface-enhanced resonance Raman scattering (SERRS) coupled with gold nanospheres was applied for rapid analysis of the hazardous substances malachite green (MG) and leucomalachite green (LMG) in fish muscle tissues. The lowest concentration of MG that could be detected was 0.5ngmL(-1) with high linear correlation (R(2)=0.970-0.998) between MG concentration and intensities of characteristic Raman peaks. A simplified sample preparation method taking less than 1h for recovering MG and LMG in fish fillets was developed for SERRS analysis, and 4-8 samples could be handled in parallel. MG and LMG could be detected in extracts of tilapia fish fillets at as low as 2ngg(-1) with SERRS and a simple principle component analysis method. For six other fish species, the lowest detectable concentration of MG ranged from 1ngg(-1) to 10ngg(-1). This study provides a new sensitive approach for the detection of trace amounts of the prohibited drugs MG and LMG in muscle food, which has the potential for rapidly screening a large number of samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

An analysis of potential stream fish and fish habitat monitoring procedures for the Inland Northwest: Annual Report 1999

Treesearch

James T. Peterson; Sherry P. Wollrab

1999-01-01

Natural resource managers in the Inland Northwest need tools for assessing the success or failure of conservation policies and the impacts of management actions on fish and fish habitats. Effectiveness monitoring is one such potential tool, but there are currently no established monitoring protocols. Since 1991, U.S. Forest Service biologists have used the standardized...

Improved utilization of fish waste by anaerobic digestion following omega-3 fatty acids extraction.

PubMed

Nges, Ivo Achu; Mbatia, Betty; Björnsson, Lovisa

2012-11-15

Fish waste is a potentially valuable resource from which high-value products can be obtained. Anaerobic digestion of the original fish waste and the fish sludge remaining after enzymatic pre-treatment to extract fish oil and fish protein hydrolysate was evaluated regarding the potential for methane production. The results showed high biodegradability of both fish sludge and fish waste, giving specific methane yields of 742 and 828 m(3)CH(4)/tons VS added, respectively. However, chemical analysis showed high concentrations of light metals which, together with high fat and protein contents, could be inhibitory to methanogenic bacteria. The feasibility of co-digesting the fish sludge with a carbohydrate-rich residue from crop production was thus investigated, and a full-scale process outlined for converting odorous fish waste to useful products. Copyright © 2012 Elsevier Ltd. All rights reserved.

Acute toxicity and effects analysis of endosulfan sulfate to freshwater fish species.

PubMed

Carriger, John F; Hoang, Tham C; Rand, Gary M; Gardinali, Piero R; Castro, Joffre

2011-02-01

Endosulfan sulfate is a persistent environmental metabolite of endosulfan, an organochlorine insecticide-acaricide presently registered by the United States Environmental Protection Agency. There is, however, limited acute fish toxicity data for endosulfan sulfate. This study determines the acute toxicity (LC₅₀s and LC₁₀s) of endosulfan sulfate to three inland Florida native fish species (mosquitofish [Gambusia affinis]; least killifish [Heterandria formosa]; and sailfin mollies [Poecilia latipinna]) as well as fathead minnows (Pimephales promelas). Ninety-six-h acute toxicity tests were conducted with each fish species under flow-through conditions. For all of the above-mentioned fish species, 96-h LC₅₀ estimates ranged from 2.1 to 3.5 μg/L endosulfan sulfate. The 96-h LC₁₀ estimates ranged from 0.8 to 2.1 μg/L endosulfan sulfate. Of all of the fish tested, the least killifish appeared to be the most sensitive to endosulfan sulfate exposure. The above-mentioned data were combined with previous acute toxicity data for endosulfan sulfate and freshwater fish for an effects analysis. The effects analysis estimated hazardous concentrations expected to exceed 5, 10, and 50% of the fish species' acute LC₅₀ or LC₁₀ values (HC₅, HC₁₀, and HC₅₀). The endosulfan sulfate freshwater-fish acute tests were also compared with the available freshwater-fish acute toxicity data for technical endosulfan. Technical endosulfan is a mixture of α- and β-endosulfan. The LC₅₀s had a wider range for technical endosulfan, and their distribution produced a lower HC₁₀ than for endosulfan sulfate. The number of freshwater-fish LC₅₀s for endosulfan sulfate is much smaller than the number available for technical endosulfan, reflecting priorities in examining the toxicity of the parent compounds of pesticides. The toxicity test results and effects analyses provided acute effect values for endosulfan sulfate and freshwater fish that might be applied in future screening level ecologic risk assessments. The effects analyses also discussed several deficiencies in conventional methods for setting water-quality criteria and determining ecologic effects from acute toxicity tests.

Out of the frying pan into the air—emersion behaviour and evaporative heat loss in an amphibious mangrove fish (Kryptolebias marmoratus)

PubMed Central

Gibson, Daniel J.; Sylvester, Emma V. A.; Turko, Andy J.; Tattersall, Glenn J.; Wright, Patricia A.

2015-01-01

Amphibious fishes often emerse (leave water) when faced with unfavourable water conditions. How amphibious fishes cope with the risks of rising water temperatures may depend, in part, on the plasticity of behavioural mechanisms such as emersion thresholds. We hypothesized that the emersion threshold is reversibly plastic and thus dependent on recent acclimation history rather than on conditions during early development. Kryptolebias marmoratus were reared for 1 year at 25 or 30°C and acclimated as adults (one week) to either 25 or 30°C before exposure to an acute increase in water temperature. The emersion threshold temperature and acute thermal tolerance were significantly increased in adult fish acclimated to 30°C, but rearing temperature had no significant effect. Using a thermal imaging camera, we also showed that emersed fish in a low humidity aerial environment (30°C) lost significantly more heat (3.3°C min−1) than those in a high humidity environment (1.6°C min−1). In the field, mean relative humidity was 84%. These results provide evidence of behavioural avoidance of high temperatures and the first quantification of evaporative cooling in an amphibious fish. Furthermore, the avoidance response was reversibly plastic, flexibility that may be important for tropical amphibious fishes under increasing pressures from climatic change. PMID:26490418

Out of the frying pan into the air--emersion behaviour and evaporative heat loss in an amphibious mangrove fish (Kryptolebias marmoratus).

PubMed

Gibson, Daniel J; Sylvester, Emma V A; Turko, Andy J; Tattersall, Glenn J; Wright, Patricia A

2015-10-01

Amphibious fishes often emerse (leave water) when faced with unfavourable water conditions. How amphibious fishes cope with the risks of rising water temperatures may depend, in part, on the plasticity of behavioural mechanisms such as emersion thresholds. We hypothesized that the emersion threshold is reversibly plastic and thus dependent on recent acclimation history rather than on conditions during early development. Kryptolebias marmoratus were reared for 1 year at 25 or 30°C and acclimated as adults (one week) to either 25 or 30°C before exposure to an acute increase in water temperature. The emersion threshold temperature and acute thermal tolerance were significantly increased in adult fish acclimated to 30°C, but rearing temperature had no significant effect. Using a thermal imaging camera, we also showed that emersed fish in a low humidity aerial environment (30°C) lost significantly more heat (3.3°C min(-1)) than those in a high humidity environment (1.6°C min(-1)). In the field, mean relative humidity was 84%. These results provide evidence of behavioural avoidance of high temperatures and the first quantification of evaporative cooling in an amphibious fish. Furthermore, the avoidance response was reversibly plastic, flexibility that may be important for tropical amphibious fishes under increasing pressures from climatic change. © 2015 The Author(s).

Serum PCB and DDE levels of frequent Great Lakes sport fish consumers -- A first look

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanrahan, L.P.; Falk, C.; Anderson, H.A.

1999-02-01

Great Lakes (GL) sport fish consumption is a potential human exposure route for polychlorinated biphenyls (PCBs) and dichlorodiphenyl dichloroethene (DDE). Because of fish tissue contamination, frequent consumers of Great Lakes sport caught fish (GLSCF) may be at risk for PCB and DDE accumulation. To examine this problem, the Health Departments of Wisconsin, Illinois, Indiana, Ohio, and Michigan formed a health assessment consortium. Participants were contacted by telephone to complete a detailed demographic and fish consumption survey. Frequent and infrequent GLSCF consumers were identified, and a participant subset was then asked to donate blood for PCB and DDE analysis. Analysis ofmore » variance (ANOVA) was done to study exposure group mean differences, while correlation and regression analyses were performed to examine relationships between demographic characteristics, GLSCF consumption, PCB, and DDE body burdens.« less

Chromosome 2 short arm translocations revealed by M-FISH analysis of neuroblastoma cell lines.

PubMed

Van Roy, N; Van Limbergen, H; Vandesompele, J; Van Gele, M; Poppe, B; Laureys, G; De Paepe, A; Speleman, F

2000-12-01

M-FISH analysis was performed on 18 neuroblastoma cell lines, which were previously studied with cytogenetic, standard FISH and CGH data. One of the most striking findings of this study was the detection of chromosome 2 short arm rearrangements in 61% of the investigated cell lines. These rearrangements resulted from translocations with various partner chromosomes. All translocations, except one were unbalanced, leading to the consistent gain of chromosome segment 2pter-p22. A cryptic balanced translocation t(2;4) was observed with a breakpoint located in the vicinity of MYCN in cell line NBL-S. Combination of M-FISH results together with cytogenetic, standard FISH and CGH data yielded the most comprehensive description of chromosome 2 short arm rearrangements, leading to a consistent gain of chromosome 2 short arm material. Copyright 2000 Wiley-Liss, Inc.

Common relationships among proximate composition components in fishes

USGS Publications Warehouse

Hartman, K.J.; Margraf, F.J.

2008-01-01

Relationships between the various body proximate components and dry matter content were examined for five species of fishes, representing anadromous, marine and freshwater species: chum salmon Oncorhynchus keta, Chinook salmon Oncorhynchus tshawytscha, brook trout Salvelinus fontinalis, bluefish Pomatomus saltatrix and striped bass Morone saxatilis. The dry matter content or per cent dry mass of these fishes can be used to reliably predict the per cent composition of the other components. Therefore, with validation it is possible to estimate fat, protein and ash content of fishes from per cent dry mass information, reducing the need for costly and time-consuming laboratory proximate analysis. This approach coupled with new methods of non-lethal estimation of per cent dry mass, such as from bioelectrical impedance analysis, can provide non-destructive measurements of proximate composition of fishes. ?? 2008 The Authors.

Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study.

PubMed

Dooley, John J; Sage, Helen D; Clarke, Marie-Anne L; Brown, Helen M; Garrett, Stephen D

2005-05-04

Identification of 10 white fish species associated with U.K. food products was achieved using PCR-RFLP of the mitochondrial cytochrome b gene. Use of lab-on-a-chip capillary electrophoresis for end-point analysis enabled accurate sizing of DNA fragments and identification of fish species at a level of 5% (w/w) in a fish admixture. One restriction enzyme, DdeI, allowed discrimination of eight species. When combined with NlaIII and HaeIII, specific profiles for all 10 species were generated. The method was applied to a range of products and subjected to an interlaboratory study carried out by five U.K. food control laboratories. One hundred percent correct identification of single species samples and six of nine admixture samples was achieved by all laboratories. The results indicated that fish species identification could be carried out using a database of PCR-RFLP profiles without the need for reference materials.

A fish on the hunt, observed neuron by neuron

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2010-01-01

This three-dimensional microscopy image reveals an output neuron of the optic tectum lighting up in response to visual information from the retina. The scientists used this state-of-the-art imaging technology to learn how neurons in the optic tectum take visual information and convert it into an output that drives action. More information: http://newscenter.lbl.gov/feature-stories/2010/10/29/zebrafish-vision/

Analysis of heavy metals (Pb and Zn) concentration in sediment of Blanakan fish ponds, Subang, West Java

NASA Astrophysics Data System (ADS)

Wiriawan, A.; Takarina, N. D.; Pin, T. G.

2017-07-01

Blanakan fish ponds receive water resource from Kali Malang and Blanakan rivers. Industrial and domestic activities along the river can cause pollution, especially heavy metals. Zinc (Zn) is an essential element that needed by an organism, while Lead (Pb) is a nonessential element that is not needed. Discharge of waste water from industries and anthropogenic activities continuously not only pollute the water but also the sediment and biota live on it. This research was aimed to know the heavy metals content in the sediment of Blanakan fish ponds. Sediment samples were taken on July and August 2016 at three locations. Heavy metals were analyzed using Atomic Absorption Spectrophotometry (AAS) Shimadzu 6300. The result of Lead (Pb) measurement showed that Fish Pond 1 had higher average concentration compared Fish Pond 2 and Fish Pond 3 which was 0.55 ppm. Standard for Lead (Pb) in sediment according to Ontario Sediment Standards (2008) is 31 ppm. Based on Zinc (Zn) measurement, it was known that average of Zinc (Zn) concentration also higher on Fish Pond 1 compared to Fish Pond 2 and 3 which was 1.93 ppm. According to Ontario Sediment Standards (2008), a standard for Zinc (Zn) in sediment is 120 ppm. This indicated that heavy metals in the sediment of fish ponds were below standards. Statistical analysis using t-test showed that there was no significant difference of heavy metals content among fish ponds.

Tetrodotoxin poisoning outbreak from imported dried puffer fish--Minneapolis, Minnesota, 2014.

PubMed

Cole, Jon B; Heegaard, William G; Deeds, Jonathan R; McGrath, Sara C; Handy, Sara M

2015-01-02

On June 13, 2014, two patients went to the Hennepin County Medical Center Emergency Department in Minneapolis, Minnesota, with symptoms suggestive of tetrodotoxin poisoning (i.e., oral paresthesias, weakness, and dyspnea) after consuming dried puffer fish (also known as globefish) purchased during a recent visit to New York City. The patients said two friends who consumed the same fish had similar, although less pronounced, symptoms and had not sought care. The Minnesota Department of Health conducted an investigation to determine the source of the product and samples were sent to the Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition for chemical and genetic analysis. Genetic analysis identified the product as puffer fish (Lagocephalus lunaris) and chemical analysis determined it was contaminated with high levels of tetrodotoxin. A traceback investigation was unable to determine the original source of the product. Tetrodotoxin is a deadly, potent poison; the minimum lethal dose in an adult human is estimated to be 2-3 mg. Tetrodotoxin is a heat-stable and acid-stable, nonprotein, alkaloid toxin found in many species of the fish family Tetraodontidae (puffer fish) as well as in certain gobies, amphibians, invertebrates, and the blue-ringed octopus. Tetrodotoxin exerts its effects by blocking voltage-activated sodium channels, terminating nerve conduction and muscle action potentials, leading to progressive paralysis and, in extreme cases, to death from respiratory failure. Because these fish were reportedly purchased in the United States, they pose a substantial U.S. public health hazard given the potency of the toxin and the high levels of toxin found in the fish.

Evaluation of Hygienic Quality and Labelling of Fish Distributed in Public Canteens of Northeast Italy

PubMed Central

Armani, Mariachiara; Civettini, Michele; Conedera, Gabriella; Favretti, Michela; Lombardo, Dorotea; Lucchini, Rosaria; Paternolli, Sabrina; Pezzuto, Alessandra; Rabini, Michela; Arcangeli, Giuseppe

2016-01-01

Over the past few years, the demand for the introduction of fish products in public canteens (schools, hospitals and nursing-homes) has grown due to their good nutritional proprieties. The particular health conditions and sensitivity of some groups of consumers exposes them to greater risks of food poisoning. It is therefore important to monitor the raw materials that end up in mass catering implementing strategies of mass catering control, both with self-monitoring strategies and with regular controls performed by the competent health authorities. The purpose of this study is to assess the overall quality of seafood dealt out from public catering services located in Northeast Italy. In this paper we illustrate the results of microbiological analysis performed on 135 fish samples (58% of samples were raw fishes, 27% cooked fishes, 6% raw fish products, 9% cooked fish products) and species identification performed on 102 fish samples. Additionally, 135 environmental swabs were collected to determine the effectiveness of cleaning and sanitation of food contact (cutting boards, cooking equipment and food processing surfaces) and non-contact (refrigerator wall and handle, tap lever) surfaces. Of raw seafood samples, 24% had total aerobic mesophilic bacteria count >105 CFU/g and for Enterobacteriaceae the faecal contamination was excluded since no Salmonella spp. and Escherichia coli were isolated. Just 3.8% of raw seafood samples resulted positive for Listeria monocytogenes. The results of swab samples of cooking utensils and surfaces showed that sanitation practices should be improved. Molecular analysis for fish species identification revealed a mislabelling for 25% of sampled fishes. The results of this survey can provide valuable information for monitoring and surveillance programmes for the control of quality of fish and fish products. PMID:27995098

Use of biomarkers in Nile tilapia (Oreochromis niloticus) to assess the impacts of pollution in Bolgoda Lake, an urban water body in Sri Lanka.

PubMed

Pathiratne, A; Chandrasekera, L W H U; Pathiratne, K A S

2009-09-01

The present study reports the first analysis of water pollutants in Sri Lankan waters using a suite of biomarkers in Nile tilapia (Oreochromis niloticus) residing in Bolgoda Lake which receives urban, industrial and domestic wastes from multiple sources. The fish were collected from the lake in the dry period (April 2005) and wet periods (September 2005, October 2006) and the levels of biomarkers viz. hepatic ethoxyresorufin O-deethylase (EROD), glutathione S-transferase (GST), metallothioneins, biliary fluorescent aromatic compounds, brain and muscle cholinesterases (ChE) were compared with those of the laboratory reared control fish and the fish obtained from a less polluted water body, Bathalagoda reservoir (reference site). The results revealed that biomarker levels of the fish collected from the reference site were not significantly different from the controls. Hepatic EROD and GST activities in fish from Bolgoda Lake were induced 4.2-16.6 folds and 1.4-3.3 folds respectively compared with the control fish. Analysis of bile in the lake fish revealed recent uptake of naphthalene, pyrene and benzo(a)pyrene type polycyclic aromatic hydrocarbons (PAHs). The induction of EROD activities in feral fish reflects the exposure of fish to aryl hydrocarbon receptor agonists including PAHs present as pollutants in the Bolgoda Lake. Cholinesterase activity in the fish inhabiting one sampling site of Bolgoda Lake was lower (22-40% inhibition) than the activity measured in the control fish indicating the presence of anticholinesterase pollutants in the area. Hepatic metallothionein levels in the lake fish were higher (1.9-3.2 folds) in comparison to the controls indicating metal exposure. The results support the potential use of these biomarkers in Nile tilapia in assessing pollution in tropical water bodies.

Ultrahigh-speed ultrahigh-resolution adaptive optics: optical coherence tomography system for in-vivo small animal retinal imaging

NASA Astrophysics Data System (ADS)

Jian, Yifan; Xu, Jing; Zawadzki, Robert J.; Sarunic, Marinko V.

2013-03-01

Small animal models of human retinal diseases are a critical component of vision research. In this report, we present an ultrahigh-resolution ultrahigh-speed adaptive optics optical coherence tomography (AO-OCT) system for small animal retinal imaging (mouse, fish, etc.). We adapted our imaging system to different types of small animals in accordance with the optical properties of their eyes. Results of AO-OCT images of small animal retinas acquired with AO correction are presented. Cellular structures including nerve fiber bundles, capillary networks and detailed double-cone photoreceptors are visualized.

Food Fish Identification from DNA Extraction through Sequence Analysis

ERIC Educational Resources Information Center

Hallen-Adams, Heather E.

2015-01-01

This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts.

PubMed

Mozaffarian, Dariush; Dashti, Hassan S; Wojczynski, Mary K; Chu, Audrey Y; Nettleton, Jennifer A; Männistö, Satu; Kristiansson, Kati; Reedik, Mägi; Lahti, Jari; Houston, Denise K; Cornelis, Marilyn C; van Rooij, Frank J A; Dimitriou, Maria; Kanoni, Stavroula; Mikkilä, Vera; Steffen, Lyn M; de Oliveira Otto, Marcia C; Qi, Lu; Psaty, Bruce; Djousse, Luc; Rotter, Jerome I; Harald, Kennet; Perola, Markus; Rissanen, Harri; Jula, Antti; Krista, Fischer; Mihailov, Evelin; Feitosa, Mary F; Ngwa, Julius S; Xue, Luting; Jacques, Paul F; Perälä, Mia-Maria; Palotie, Aarno; Liu, Yongmei; Nalls, Nike A; Ferrucci, Luigi; Hernandez, Dena; Manichaikul, Ani; Tsai, Michael Y; Kiefte-de Jong, Jessica C; Hofman, Albert; Uitterlinden, André G; Rallidis, Loukianos; Ridker, Paul M; Rose, Lynda M; Buring, Julie E; Lehtimäki, Terho; Kähönen, Mika; Viikari, Jorma; Lemaitre, Rozenn; Salomaa, Veikko; Knekt, Paul; Metspalu, Andres; Borecki, Ingrid B; Cupples, L Adrienne; Eriksson, Johan G; Kritchevsky, Stephen B; Bandinelli, Stefania; Siscovick, David; Franco, Oscar H; Deloukas, Panos; Dedoussis, George; Chasman, Daniel I; Raitakari, Olli; Tanaka, Toshiko

2017-01-01

Regular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences. To identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption. We conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts. Heritability estimates for fish and EPA+DHA consumption ranged from 0.13-0.24 and 0.12-0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA. These novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation.

  Ultrasonic monitoring of fish thawing process optimal time of thawing and effect of freezing/thawing.

PubMed

El Kadi, Youssef Ait; Moudden, Ali; Faiz, Bouazza; Maze, Gerard; Decultot, Dominique

2013-01-01

Fish quality is traditionally controlled by chemical and microbiological analysis. The non-destructive control presents an enormous professional interest thanks to the technical contribution and precision of the analysis to which it leads. This paper presents the results obtained from a characterisation of fish thaw-ing process by the ultrasonic technique, with monitoring thermal processing from frozen to defrosted states. The study was carried out on fish type red drum and salmon cut into fillets of 15 mm thickness. After being frozen at -20°C, the sample is enclosed in a plexiglas vessel with parallel walls at the ambient temperature 30°C and excited in perpendicular incidence at 0.5 MHz by an ultrasonic pulser-receiver Sofranel 5052PR. the technique of measurement consists to study the signals reflected by fish during its thawing, the specific techniques of signal processing are implemented to deduce informations characterizing the state of fish and its thawing process by examining the evolution of the position echoes reflected by the sample and the viscoelastic parameters of fish during its thawing. The obtained results show a relationship between the thermal state of fish and its acoustic properties, which allowed to deduce the optimal time of the first thawing in order to restrict the growth of microbial flora. For salmon, the results show a decrease of 36% of the time of the second thawing and an increase of 10.88% of the phase velocity, with a decrease of 65.5% of the peak-to-peak voltage of the signal reflected, thus a decrease of the acoustic impedance. This study shows an optimal time and an evolution rate of thawing specific to each type offish and a correlation between the acoustic behavior of fish and its thermal state which approves that this technique of ultrasonic monitoring can substitute the control using the destructive chemical analysis in order to monitor the thawing process and to know whether a fish has suffered an accidental thawing.

Hydroacoustic Assessment of Behavioral Responses by Fish Passing Near an Operating Tidal Turbine in the East River, New York

DOE PAGES

Bevelhimer, Mark; Scherelis, Constantin C.; Colby, Jonathan; ...

2017-06-13

An important environmental issue facing the marine and hydrokinetic energy industry is whether fish that encounter underwater energy devices are likely to be struck and injured by moving components, primarily rotating turbine blades. The automated analysis of nearly 3 weeks of multibeam hydroacoustics data identified about 35,000 tracks of fish passing a tidal turbine in the East River, New York. These tracks included both individual fish and schools during periods with the turbine absent, the turbine present and operating, and the turbine present but not operating. The density of fish in the sampled area when the turbine was absent wasmore » roughly twice the density observed when the turbine was in place, particularly when the turbine was operating. This suggests that some avoidance occurred before fish were close enough to the turbine to be observed by the hydroacoustics system. Various measures of swimming behavior (direction, velocity, and linearity) were calculated for each track and evaluated for indication of behavioral responses to turbine presence and operation. Fish tracks were grouped based on tidal cycle, current velocity, and swimming direction and were evaluated with respect to turbine presence and operation and with respect to distance from the turbine. Nonparametric tests (Kolmogorov–Smirnov test) and multivariate analysis (canonical discriminant analysis) found significant differences among groups with respect to turbine presence and operation, suggesting that some fish responded to the turbine by adjusting swimming behavior, such as making small adjustments to swimming direction and velocity as they passed near the turbine. We found no evidence that fish were being struck by rotating blades, but there did appear to be large-scale avoidance initiated out of the range of the hydroacoustics detection system. Furthermore, more study is needed to determine whether such avoidance behavior has significant ramifications for normal fish movement patterns, bioenergetics, seasonal migrations, and predator exposure.« less

Hydroacoustic Assessment of Behavioral Responses by Fish Passing Near an Operating Tidal Turbine in the East River, New York

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bevelhimer, Mark; Scherelis, Constantin C.; Colby, Jonathan

An important environmental issue facing the marine and hydrokinetic energy industry is whether fish that encounter underwater energy devices are likely to be struck and injured by moving components, primarily rotating turbine blades. The automated analysis of nearly 3 weeks of multibeam hydroacoustics data identified about 35,000 tracks of fish passing a tidal turbine in the East River, New York. These tracks included both individual fish and schools during periods with the turbine absent, the turbine present and operating, and the turbine present but not operating. The density of fish in the sampled area when the turbine was absent wasmore » roughly twice the density observed when the turbine was in place, particularly when the turbine was operating. This suggests that some avoidance occurred before fish were close enough to the turbine to be observed by the hydroacoustics system. Various measures of swimming behavior (direction, velocity, and linearity) were calculated for each track and evaluated for indication of behavioral responses to turbine presence and operation. Fish tracks were grouped based on tidal cycle, current velocity, and swimming direction and were evaluated with respect to turbine presence and operation and with respect to distance from the turbine. Nonparametric tests (Kolmogorov–Smirnov test) and multivariate analysis (canonical discriminant analysis) found significant differences among groups with respect to turbine presence and operation, suggesting that some fish responded to the turbine by adjusting swimming behavior, such as making small adjustments to swimming direction and velocity as they passed near the turbine. We found no evidence that fish were being struck by rotating blades, but there did appear to be large-scale avoidance initiated out of the range of the hydroacoustics detection system. Furthermore, more study is needed to determine whether such avoidance behavior has significant ramifications for normal fish movement patterns, bioenergetics, seasonal migrations, and predator exposure.« less

Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts

PubMed Central

Dashti, Hassan S; Wojczynski, Mary K; Chu, Audrey Y; Nettleton, Jennifer A; Männistö, Satu; Kristiansson, Kati; Reedik, Mägi; Lahti, Jari; Houston, Denise K; Cornelis, Marilyn C; van Rooij, Frank J. A; Dimitriou, Maria; Kanoni, Stavroula; Mikkilä, Vera; Steffen, Lyn M; de Oliveira Otto, Marcia C; Qi, Lu; Psaty, Bruce; Djousse, Luc; Rotter, Jerome I; Harald, Kennet; Perola, Markus; Rissanen, Harri; Jula, Antti; Krista, Fischer; Mihailov, Evelin; Feitosa, Mary F; Ngwa, Julius S; Xue, Luting; Jacques, Paul F; Perälä, Mia-Maria; Palotie, Aarno; Liu, Yongmei; Nalls, Nike A; Ferrucci, Luigi; Hernandez, Dena; Manichaikul, Ani; Tsai, Michael Y; Kiefte-de Jong, Jessica C; Hofman, Albert; Uitterlinden, André G; Rallidis, Loukianos; Ridker, Paul M; Rose, Lynda M; Buring, Julie E; Lehtimäki, Terho; Kähönen, Mika; Viikari, Jorma; Lemaitre, Rozenn; Salomaa, Veikko; Knekt, Paul; Metspalu, Andres; Borecki, Ingrid B; Cupples, L. Adrienne; Eriksson, Johan G; Kritchevsky, Stephen B; Bandinelli, Stefania; Siscovick, David; Franco, Oscar H; Deloukas, Panos; Dedoussis, George; Chasman, Daniel I; Raitakari, Olli; Tanaka, Toshiko

2017-01-01

Background Regular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences. Objective To identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption. Design We conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts. Results Heritability estimates for fish and EPA+DHA consumption ranged from 0.13–0.24 and 0.12–0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA. Conclusions These novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation. PMID:29236708

Landscape-scale food webs of fish nursery habitat along a river-coast mixing zone

EPA Science Inventory

We used carbon and nitrogen stable isotope analysis to study connections between allochthonous energy use and ecological connectivity of fish larvae in a complex coastal mosaic. We quantified fish larvae support by autochthonous and allochthonous material in three coastal river-w...

Fish Viruses: Buffers and Methods for Plaquing Eight Agents Under Normal Atmosphere

PubMed Central

Wolf, Ken; Quimby, M. C.

1973-01-01

A universal procedure was sought for plaque assay of eight fish viruses (bluegill myxovirus, channel catfish virus, eel virus, Egtved virus, infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, lymphocystis virus, and the agent of spring viremia of carp (Rhabdovirus carpio), in dish cultures of various fish cells. Eagle minimal essential medium with sodium bicarbonate-CO2 buffer (Earle’s salt solution) was compared with minimal essential medium buffered principally with tris (hydroxymethyl)aminomethane or N-2-hydroxyethylpiperazine-N′-2′-ethanesulfonic acid at a pH or in the range of 7.6 to 8.0 depending upon temperature. Five fish cell lines collectively capable of replicating all fish viruses thus far isolated were tested and quantitatively found to grow comparably well in the three media. Two-phase (gel-liquid) media incorporating the various buffer systems allowed plaquing at 15 to 33 C either in partial pressures of CO2 or in normal atmosphere, but greater efficiency and sensitivity were obtained with the organic buffers, and, overall, the best results were obtained with tris(hydroxymethyl)aminomethane. Epizootiological data, specific fish cell line response, and plaque morphology permit presumptive identification of most of the agents. At proper pH, use of organic buffers obviates the need for CO2 incubators. Images PMID:4349252

Long-term changes in fish communities of the Ria Formosa coastal lagoon (southern Portugal) based on two studies made 20 years apart

NASA Astrophysics Data System (ADS)

Ribeiro, Joaquim; Monteiro, Carlos C.; Monteiro, Pedro; Bentes, Luis; Coelho, Rui; Gonçalves, Jorge M. S.; Lino, Pedro G.; Erzini, Karim

2008-01-01

Fish communities of the Ria Formosa coastal lagoon (south Portugal) were sampled on a monthly basis with a beach seine at 4 sites, during two different time periods: 1980-1986 and 2001-2002. Community indices, species ranking and multivariate analysis were used in order to identify changes in the fish community between the two time periods. A total of 153,511 fish representing 57 taxa were recorded. Although species composition was very similar for both sampling periods, multivariate analysis performed on annual species abundance in number and weight revealed differences in fish community structure between the two periods. Structural changes in fish community were related mostly to a sharp decrease in the abundance of Mugilidae from 1980-1986 to 2001-2002. These changes were probably associated to a decrease in organic matter contents and nutrients concentrations due to improvements in sewage treatment and better water circulation inside the lagoon. The changes in fish community structure are more evident in the inner areas of the lagoon than near the inlet. The association between changes in sewage patterns and changes in the ichthyofaunal community structure reinforces the importance of fish communities as a biological indicator of human induced changes in marine systems.

Perceptions of fish habitat conditions in Oklahoma tailwater fisheries: a survey of fisheries managers

USGS Publications Warehouse

Long, James M.

2011-01-01

While the downstream effects of dams on fish habitat have long been recognized, broad-scale assessments of tailwater fish habitat have rarely been conducted. In this paper, I report on the status of tailwater fisheries in Oklahoma as determined through a web-based survey of fisheries biologists with the Oklahoma Department of Wildlife Conservation conducted in July 2010. Respondents addressed 38 tailwaters, encompassing all major areas of the state. The majority of fish species comprising these fisheries included blue catfish (Ictalurus furcatus), followed by white bass (Morone chrysops), channel catfish (I. punctatus) and flathead catfish (Pylodictis olivaris). Most respondents indicated no or low concerns with fish habitat in tailwaters under their management supervision; only two tailwaters (Tenkiller Ferry and Fort Gibson) had the majority of concerns with fish habitat identified as high to moderately high. Principal components analysis and subsequent correlation analysis showed that tailwaters that scored high for issues related to shoreline erosion, change in water depth, flow fluctuations, and flow timing were associated with dams with large maximum discharge ability. No other factors related to fish habitat condition in tailwaters were found. In Oklahoma, dams with maximum discharge of at least 6,767.5 m3 sec–1 were more likely to have flow-related fish habitat concerns in the tailwater.

SE Asian freshwater fish population and networks: the impacts of climatic and environmental change on a vital resource

NASA Astrophysics Data System (ADS)

Santos, Rita; Parsons, Daniel; Cowx, Ian

2016-04-01

The Mekong River is the 10th largest freshwater river in the world, with the second highest biodiversity wealth, behind the much larger Amazon basin. The fisheries activity in the Lower Mekong countries counts for 2.7 million tons of fish per year, with an estimated value worth up to US 7 billion. For the 60 million people living in the basin, fish represent their primary source of economic income and protein intake, with an average per capita consumption estimated at 45.4 Kg. The proposed hydropower development in the basin is threatening its sustainability and resilience. Such developments affect fish migration patterns, hydrograph flood duration and magnitudes and sediment flux. Climate change is also likely to impact the basin, exacerbating the issues created by development. As a monsoonal system, the Mekong River's pronounced annual flood pulse cycle is important in creating variable habitat for fish productivity. Moreover, the annual flood also triggers fish migration and provides vital nutrients carried by the sediment flux. This paper examines the interactions between both dam development and climate change scenarios on fish habitat and habitat connectivity, with the aim of predicting how these will affect fish species composition and fisheries catch. The project will also employ Environmental DNA (eDNA) to quantify and understand the species composition of this complex and large freshwater system. By applying molecular analysis, it is possible to trace species abundance and migration patterns of fish and evaluate the ecological networks establish between an inland system. The aim of this work is to estimate, using process-informed models, the impacts of the proposed dam development and climate change scenarios on the hydrological and hydraulic conditions of habitat availability for fish. Furthermore, it will evaluate the connectivity along the Mekong and its tributaries, and the importance of maintaining these migration pathways, used by a great diversity of fish species. It will also present the preliminary findings on eDNA analysis for species composition and the ecological networks established along the river and particularly on the fish hotspot place for biodiversity, the Tonle Sap system in Cambodia. Keywords: Mekong River, climate change, fish production, dams, eDNA analysis, numerical modelling.

To develop a flying fish egg inspection system by a digital imaging base system

NASA Astrophysics Data System (ADS)

Chen, Chun-Jen; Jywe, Wenyuh; Hsieh, Tung-Hsien; Chen, Chien Hung

2015-07-01

This paper develops an automatic optical inspection system for flying fish egg quality inspection. The automatic optical inspection system consists of a 2-axes stage, a digital camera, a lens, a LED light source, a vacuum generator, a tube and a tray. This system can automatically find the particle on the flying egg tray and used stage to driver the tube onto the particle. Then use straw and vacuum generator to pick up the particle. The system pick rate is about 30 particles per minute.

Maturation and fecundity of a stock-enhanced population of striped bass in the Savannah River Estuary, U.S.A.

USGS Publications Warehouse

Will, T.A.; Reinert, T.R.; Jennings, C.A.

2002-01-01

The striped bass Morone saxatilis population in the Savannah River (south-eastern U.S.A.) collapsed in the 1980s, and recent efforts to restore the population have resulted in increased catch-per-unit-effort (CPUE) of striped bass in the Savannah River Estuary (SRE). The abundance of eggs and larvae, however, remain well below historic levels. The primary cause of the population decline was remedied, and environmental conditions seem suitable for striped bass spawning. Regression analysis of data derived from ultrasonic imaging of 31 striped bass resulted in a statistical model that predicted ovary volume well (r2=0.95). The enumeration of oocytes from ovarian tissue samples and the prediction of ovary volume allowed fecundity to be estimated without sacrificing the fish. Oocyte maturation in Savannah River striped bass seemed to progress normally, with oocytes developing to final stages of maturity in larger fish (>750 mm LT). Additionally, fecundity estimates were comparable to a neighbouring striped bass population. The environmental cues needed to trigger development and release of striped bass oocytes into the SRE appeared to be present. If most of the striped bass females in the SRE are still young (<7 years), the ability to produce large numbers of eggs will be limited. As these young fish mature, egg production probably will increase and the density of striped bass eggs eventually will approach historic levels, provided suitable habitat and water quality are maintained. ?? 2002 The Fisheries Society of the British Isles.

The impact of glide phases on the trackability of hydrodynamic trails in harbour seals (Phoca vitulina).

PubMed

Wieskotten, S; Dehnhardt, G; Mauck, B; Miersch, L; Hanke, W

2010-11-01

The mystacial vibrissae of harbour seals (Phoca vitulina) constitute a highly sensitive hydrodynamic receptor system enabling the seals to detect and follow hydrodynamic trails. In the wild, hydrodynamic trails, as generated by swimming fish, consist of cyclic burst-and-glide phases, associated with various differences in the physical parameters of the trail. Here, we investigated the impact of glide phases on the trackability of differently aged hydrodynamic trails in a harbour seal. As fish are not easily trained to swim certain paths with predetermined burst-and-glide phases, the respective hydrodynamic trails were generated using a remote-controlled miniature submarine. Gliding phases in hydrodynamic trails had a negative impact on the trackability when trails were 15 s old. The seal lost the generated trails more often within the transition zones, when the submarine switched from a burst to a glide moving pattern. Hydrodynamic parameter analysis (particle image velocimetry) revealed that the smaller dimensions and faster decay of hydrodynamic trails generated by the gliding submarine are responsible for the impaired success of the seal tracking the gliding phase. Furthermore, the change of gross water flow generated by the submarine from a rearwards-directed stream in the burst phase to a water flow passively dragged behind the submarine during gliding might influence the ability of the seal to follow the trail as this might cause a weaker deflection of the vibrissae. The possible ecological implications of intermittent swimming behaviour in fish for piscivorous predators are discussed.

Measuring flow velocity and flow direction by spatial and temporal analysis of flow fluctuations.

PubMed

Chagnaud, Boris P; Brücker, Christoph; Hofmann, Michael H; Bleckmann, Horst

2008-04-23

If exposed to bulk water flow, fish lateral line afferents respond only to flow fluctuations (AC) and not to the steady (DC) component of the flow. Consequently, a single lateral line afferent can encode neither bulk flow direction nor velocity. It is possible, however, for a fish to obtain bulk flow information using multiple afferents that respond only to flow fluctuations. We show by means of particle image velocimetry that, if a flow contains fluctuations, these fluctuations propagate with the flow. A cross-correlation of water motion measured at an upstream point with that at a downstream point can then provide information about flow velocity and flow direction. In this study, we recorded from pairs of primary lateral line afferents while a fish was exposed to either bulk water flow, or to the water motion caused by a moving object. We confirm that lateral line afferents responded to the flow fluctuations and not to the DC component of the flow, and that responses of many fiber pairs were highly correlated, if they were time-shifted to correct for gross flow velocity and gross flow direction. To prove that a cross-correlation mechanism can be used to retrieve the information about gross flow velocity and direction, we measured the flow-induced bending motions of two flexible micropillars separated in a downstream direction. A cross-correlation of the bending motions of these micropillars did indeed produce an accurate estimate of the velocity vector along the direction of the micropillars.

AN ANALYSIS OF THE INFLUENCE OF ANNUAL THERMAL VARIABLES ON THE OCCURRENCE OF WARM WATER FISHES

EPA Science Inventory

A potential effect of climate change is modification of the geographic distribution of fish species. To predict this modification it is necessary to estimate temperature tolerances of fishes and then relate these tolerances to the changing environment. This technique will allow...

MERCURY CONCENTRATION IN FROZEN WHOLE-FISH HOMOGENATES IS INSENSITIVE TO HOLDING TIME

EPA Science Inventory

Current recommended holding times for the analysis of total mercury (Hg) in fish tissue ranges from 28 to 180 days. In 2006, we evaluated the effect of an extended holding time on Hg concentrations by reanalyzing whole-fish wet homogenates that were analyzed originally in 2002 an...

Pathway-based Analysis of Fish Transcriptomics Data across Effluent Gradients in Minnesota Rivers

EPA Science Inventory

As part of a larger effort to assess the health of streams and rivers in Minnesota, a series of caged fish experiments were conducted in three locations: Ely, Hutchinson, and Rochester. The experimental design placed caged fish (fathead minnows, Pimephales promelas; FHM) across ...

FISH-ing for Genes: Modeling Fluorescence "in situ" Hybridization

ERIC Educational Resources Information Center

Baker, William P.; Jones, Carleton Buck

2006-01-01

Teaching methods of genetic analysis such as fluorescence in situ hybridization (FISH) can be an important part of instructional units in biology, microbiology, and biotechnology. Experience, however, indicates that these topics are difficult for many students. The authors of this article describe how they created an activity that effectively…

77 FR 16540 - New England Fishery Management Council; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-21

... development and analysis in Omnibus Essential Fish Habitat Amendment 2. Two types of measures will be considered at the meeting: (1) Options to minimize the adverse effects of fishing on Essential Fish Habitat... England Fishery Management Council (Council) is scheduling a public meeting of its Habitat Oversight...

76 FR 15301 - Pacific Fishery Management Council; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-21

... Council Direction for 2011 Management Measures for Analysis 5. Essential Fish Habitat Review 6. Adoption... Review 3. Periodic Essential Fish Habitat Review Process 4. Formation of Risk Pools under the Trawl... Service Report 2. Exempted Fishing Permit for 2011 Aerial Survey 3. CPS Survey Methodology D. Habitat...

77 FR 5774 - New England Fishery Management Council; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... management measures for further development and analysis in Omnibus Essential Fish Habitat Amendment 2. Two... fishing on Essential Fish Habitat and (2) alternatives to protect deep-sea corals from the impacts of... England Fishery Management Council (Council) is scheduling a public meeting of its Habitat/MPA/Ecosystem...

Genetic analysis and antimicrobial susceptibility of Francisella noatunensis subsp. orientalis (sun. F. asiatica) isolates from fish

USDA-ARS?s Scientific Manuscript database

Francisella noatunensis subsp. orientalis (syn. F. asiatica) (Fno) is an emergent fish pathogen that causes acute to chronic disease in a wide variety of freshwater, brackish and marine fish. Due to the emergent nature of this bacterium, established protocols to measure antimicrobial susceptibility ...

STATISTICAL TECHNIQUES FOR DETERMINATION AND PREDICTION OF FUNDAMENTAL FISH ASSEMBLAGES OF THE MID-ATLANTIC HIGHLANDS

EPA Science Inventory

A statistical software tool, Stream Fish Community Predictor (SFCP), based on EMAP stream sampling in the mid-Atlantic Highlands, was developed to predict stream fish communities using stream and watershed characteristics. Step one in the tool development was a cluster analysis t...

Analysis of stable isotopes in fish to identify habitat use and switching

EPA Science Inventory

In our isotopic studies of fish in Oregon Coast Range streams we have found stable isotopes of carbon, oxygen and sulfur to be surprisingly useful in identifying and discriminating specific habitat or tributary use by a variety of fish species. Stable isotopes of carbon can be u...

Relationship among side channels, fish assemblages, and environmental gradients in the unimpounded Upper Mississippi River

USGS Publications Warehouse

Barko, V.A.; Herzog, D.P.

2003-01-01

We analyzed fish abundance and environmental data collected over nine years from six side channels of the unimpounded upper Mississippi River between river km 46.7 and 128.7. A partial canonical correspondence analysis revealed differences in fish assemblages and environmental factors correlated with the six side channels. Fishes correlated with open side channels represented large river species tolerant of current and/or turbidity. Fishes correlated with closed side channels represented assemblages preferring either moderate to low turbidity/current or pools.

Effects of docosahexaenoic acid and methylmercury on child's brain development due to consumption of fish by Finnish mother during pregnancy: a probabilistic modeling approach.

PubMed

Leino, O; Karjalainen, A K; Tuomisto, J T

2013-04-01

Fish contains both beneficial substances e.g. docosahexaenoic acids but also harmful compounds e.g. methylmercury. Importantly, the health effects caused by these two substances can be evaluated in one common end point, intelligence quotient (IQ), providing a more transparent analysis. We estimated health effects of maternal fish consumption on child's central nervous system by creating a model with three alternative maternal fish consumption scenarios (lean fish, fatty fish, and current fish consumption). Additionally, we analyzed impacts of both regular fish consumption and extreme fish consumption habits. At the individual level, the simulated net effects were small, encompassing a range of one IQ point in all scenarios. Fatty fish consumption, however, clearly generated a beneficial net IQ effect, and lean fish consumption evoked an adverse net IQ effect. In view of the current fish consumption pattern of Finnish mothers the benefits and risks seem to more or less compensate each other. This study clearly shows the significance of which fish species are consumed during pregnancy and lactation, and the results can be generalized to apply to typical western population fish consumption habits. Copyright © 2011 Elsevier Ltd. All rights reserved.

Rapid estimation of microbial populations in fish samples by using terminal restriction fragment length polymorphism analysis of 16S rDNA.

PubMed

Tanaka, Yuichiro; Takahashi, Hajime; Kitazawa, Nao; Kimura, Bon

2010-01-01

A rapid system using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting 16S rDNA is described for microbial population analysis in edible fish samples. The defined terminal restriction fragment database was constructed by collecting 102 strains of bacteria representing 53 genera that are associated with fish. Digestion of these 102 strains with two restriction enzymes, HhaI and MspI, formed 54 pattern groups with discrimination to the genus level. This T-RFLP system produced results comparable to those from a culture-based method in six natural fish samples with a qualitative correspondence of 71.4 to 92.3%. Using the T-RFLP system allowed an estimation of the microbial population within 7 h. Rapid assay of the microbial population is advantageous for food manufacturers and testing laboratories; moreover, the strategy presented here allows adaptation to specific testing applications.

Household economic modelsof gill net fishermen at Madura strait

NASA Astrophysics Data System (ADS)

Primyastanto, M.

2018-04-01

The purposes of this research was to analyze household economic models of gill net fishermen at Madura strait. 30 families of gillnet fishermenwere used for purposive sampling. Data analysis used descriptive qualitative and quantitative (regression analysis). Quantitative descriptive analysis was used to analyze research and compare to factors that affecting household economic models of gill net fishermen family. Research results showed tha thousehold economic models of gill net fishermen at Madura strait was production value level or fishermen revenue at sea was strongly influenced byp roduction asset production, education level, fuel, and work flow. Work flow rate of fishermen families affected by asset production, non fisheries workflow and number of male workforce. Non fishing income level was strongly influenced by non-fishery business assets, number of family members owned andnon-fishing work flow. Spending levels of gill net fishermen at Madura strait was affected by fishing income, non-fishing income, fishermen wife education and fishermen family members.

LARVAL FISH HABITAT QUALITY : THE EFFECTS OF FRESHWATER FLOW

EPA Science Inventory

We sampled larval fish in Suisun Marsh, in the San Francisco Bay estuary from February to June 1994-1999. We used principal components analysis (PCA) and canonical correspondence analysis (CCA) on 13 taxonomic groups making up 99.7% of the catch and several environmental variable...