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.

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

Mobile sailing robot for automatic estimation of fish density and monitoring water quality

PubMed Central

2013-01-01

Introduction The paper presents the methodology and the algorithm developed to analyze sonar images focused on fish detection in small water bodies and measurement of their parameters: volume, depth and the GPS location. The final results are stored in a table and can be exported to any numerical environment for further analysis. Material and method The measurement method for estimating the number of fish using the automatic robot is based on a sequential calculation of the number of occurrences of fish on the set trajectory. The data analysis from the sonar concerned automatic recognition of fish using the methods of image analysis and processing. Results Image analysis algorithm, a mobile robot together with its control in the 2.4 GHz band and full cryptographic communication with the data archiving station was developed as part of this study. For the three model fish ponds where verification of fish catches was carried out (548, 171 and 226 individuals), the measurement error for the described method was not exceeded 8%. Summary Created robot together with the developed software has features for remote work also in the variety of harsh weather and environmental conditions, is fully automated and can be remotely controlled using Internet. Designed system enables fish spatial location (GPS coordinates and the depth). The purpose of the robot is a non-invasive measurement of the number of fish in water reservoirs and a measurement of the quality of drinking water consumed by humans, especially in situations where local sources of pollution could have a significant impact on the quality of water collected for water treatment for people and when getting to these places is difficult. The systematically used robot equipped with the appropriate sensors, can be part of early warning system against the pollution of water used by humans (drinking water, natural swimming pools) which can be dangerous for their health. PMID:23815984

Mobile sailing robot for automatic estimation of fish density and monitoring water quality.

PubMed

Koprowski, Robert; Wróbel, Zygmunt; Kleszcz, Agnieszka; Wilczyński, Sławomir; Woźnica, Andrzej; Łozowski, Bartosz; Pilarczyk, Maciej; Karczewski, Jerzy; Migula, Paweł

2013-07-01

The paper presents the methodology and the algorithm developed to analyze sonar images focused on fish detection in small water bodies and measurement of their parameters: volume, depth and the GPS location. The final results are stored in a table and can be exported to any numerical environment for further analysis. The measurement method for estimating the number of fish using the automatic robot is based on a sequential calculation of the number of occurrences of fish on the set trajectory. The data analysis from the sonar concerned automatic recognition of fish using the methods of image analysis and processing. Image analysis algorithm, a mobile robot together with its control in the 2.4 GHz band and full cryptographic communication with the data archiving station was developed as part of this study. For the three model fish ponds where verification of fish catches was carried out (548, 171 and 226 individuals), the measurement error for the described method was not exceeded 8%. Created robot together with the developed software has features for remote work also in the variety of harsh weather and environmental conditions, is fully automated and can be remotely controlled using Internet. Designed system enables fish spatial location (GPS coordinates and the depth). The purpose of the robot is a non-invasive measurement of the number of fish in water reservoirs and a measurement of the quality of drinking water consumed by humans, especially in situations where local sources of pollution could have a significant impact on the quality of water collected for water treatment for people and when getting to these places is difficult. The systematically used robot equipped with the appropriate sensors, can be part of early warning system against the pollution of water used by humans (drinking water, natural swimming pools) which can be dangerous for their health.

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.

Induction of Social Behavior in Zebrafish: Live Versus Computer Animated Fish as Stimuli

PubMed Central

Qin, Meiying; Wong, Albert; Seguin, Diane

2014-01-01

Abstract The zebrafish offers an excellent compromise between system complexity and practical simplicity and has been suggested as a translational research tool for the analysis of human brain disorders associated with abnormalities of social behavior. Unlike laboratory rodents zebrafish are diurnal, thus visual cues may be easily utilized in the analysis of their behavior and brain function. Visual cues, including the sight of conspecifics, have been employed to induce social behavior in zebrafish. However, the method of presentation of these cues and the question of whether computer animated images versus live stimulus fish have differential effects have not been systematically analyzed. Here, we compare the effects of five stimulus presentation types: live conspecifics in the experimental tank or outside the tank, playback of video-recorded live conspecifics, computer animated images of conspecifics presented by two software applications, the previously employed General Fish Animator, and a new application Zebrafish Presenter. We report that all stimuli were equally effective and induced a robust social response (shoaling) manifesting as reduced distance between stimulus and experimental fish. We conclude that presentation of live stimulus fish, or 3D images, is not required and 2D computer animated images are sufficient to induce robust and consistent social behavioral responses in zebrafish. PMID:24575942

Induction of social behavior in zebrafish: live versus computer animated fish as stimuli.

PubMed

Qin, Meiying; Wong, Albert; Seguin, Diane; Gerlai, Robert

2014-06-01

The zebrafish offers an excellent compromise between system complexity and practical simplicity and has been suggested as a translational research tool for the analysis of human brain disorders associated with abnormalities of social behavior. Unlike laboratory rodents zebrafish are diurnal, thus visual cues may be easily utilized in the analysis of their behavior and brain function. Visual cues, including the sight of conspecifics, have been employed to induce social behavior in zebrafish. However, the method of presentation of these cues and the question of whether computer animated images versus live stimulus fish have differential effects have not been systematically analyzed. Here, we compare the effects of five stimulus presentation types: live conspecifics in the experimental tank or outside the tank, playback of video-recorded live conspecifics, computer animated images of conspecifics presented by two software applications, the previously employed General Fish Animator, and a new application Zebrafish Presenter. We report that all stimuli were equally effective and induced a robust social response (shoaling) manifesting as reduced distance between stimulus and experimental fish. We conclude that presentation of live stimulus fish, or 3D images, is not required and 2D computer animated images are sufficient to induce robust and consistent social behavioral responses in zebrafish.

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.

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.

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.

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

FISH Finder: a high-throughput tool for analyzing FISH images

PubMed Central

Shirley, James W.; Ty, Sereyvathana; Takebayashi, Shin-ichiro; Liu, Xiuwen; Gilbert, David M.

2011-01-01

Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes. Availability: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list Contact: gilbert@bio.fsu.edu PMID:21310746

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.

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.

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.

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.

Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.

PubMed

Valm, Alex M; Mark Welch, Jessica L; Rieken, Christopher W; Hasegawa, Yuko; Sogin, Mitchell L; Oldenbourg, Rudolf; Dewhirst, Floyd E; Borisy, Gary G

2011-03-08

Microbes in nature frequently function as members of complex multitaxon communities, but the structural organization of these communities at the micrometer level is poorly understood because of limitations in labeling and imaging technology. We report here a combinatorial labeling strategy coupled with spectral image acquisition and analysis that greatly expands the number of fluorescent signatures distinguishable in a single image. As an imaging proof of principle, we first demonstrated visualization of Escherichia coli labeled by fluorescence in situ hybridization (FISH) with 28 different binary combinations of eight fluorophores. As a biological proof of principle, we then applied this Combinatorial Labeling and Spectral Imaging FISH (CLASI-FISH) strategy using genus- and family-specific probes to visualize simultaneously and differentiate 15 different phylotypes in an artificial mixture of laboratory-grown microbes. We then illustrated the utility of our method for the structural analysis of a natural microbial community, namely, human dental plaque, a microbial biofilm. We demonstrate that 15 taxa in the plaque community can be imaged simultaneously and analyzed and that this community was dominated by early colonizers, including species of Streptococcus, Prevotella, Actinomyces, and Veillonella. Proximity analysis was used to determine the frequency of inter- and intrataxon cell-to-cell associations which revealed statistically significant intertaxon pairings. Cells of the genera Prevotella and Actinomyces showed the most interspecies associations, suggesting a central role for these genera in establishing and maintaining biofilm complexity. The results provide an initial systems-level structural analysis of biofilm organization.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Wavelet-based compression of M-FISH images.

PubMed

Hua, Jianping; Xiong, Zixiang; Wu, Qiang; Castleman, Kenneth R

2005-05-01

Multiplex fluorescence in situ hybridization (M-FISH) is a recently developed technology that enables multi-color chromosome karyotyping for molecular cytogenetic analysis. Each M-FISH image set consists of a number of aligned images of the same chromosome specimen captured at different optical wavelength. This paper presents embedded M-FISH image coding (EMIC), where the foreground objects/chromosomes and the background objects/images are coded separately. We first apply critically sampled integer wavelet transforms to both the foreground and the background. We then use object-based bit-plane coding to compress each object and generate separate embedded bitstreams that allow continuous lossy-to-lossless compression of the foreground and the background. For efficient arithmetic coding of bit planes, we propose a method of designing an optimal context model that specifically exploits the statistical characteristics of M-FISH images in the wavelet domain. Our experiments show that EMIC achieves nearly twice as much compression as Lempel-Ziv-Welch coding. EMIC also performs much better than JPEG-LS and JPEG-2000 for lossless coding. The lossy performance of EMIC is significantly better than that of coding each M-FISH image with JPEG-2000.

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.

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.

An effective and robust method for tracking multiple fish in video image based on fish head detection.

PubMed

Qian, Zhi-Ming; Wang, Shuo Hong; Cheng, Xi En; Chen, Yan Qiu

2016-06-23

Fish tracking is an important step for video based analysis of fish behavior. Due to severe body deformation and mutual occlusion of multiple swimming fish, accurate and robust fish tracking from video image sequence is a highly challenging problem. The current tracking methods based on motion information are not accurate and robust enough to track the waving body and handle occlusion. In order to better overcome these problems, we propose a multiple fish tracking method based on fish head detection. The shape and gray scale characteristics of the fish image are employed to locate the fish head position. For each detected fish head, we utilize the gray distribution of the head region to estimate the fish head direction. Both the position and direction information from fish detection are then combined to build a cost function of fish swimming. Based on the cost function, global optimization method can be applied to associate the target between consecutive frames. Results show that our method can accurately detect the position and direction information of fish head, and has a good tracking performance for dozens of fish. The proposed method can successfully obtain the motion trajectories for dozens of fish so as to provide more precise data to accommodate systematic analysis of fish behavior.

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

Real-time color/shape-based traffic signs acquisition and recognition system

NASA Astrophysics Data System (ADS)

Saponara, Sergio

2013-02-01

A real-time system is proposed to acquire from an automotive fish-eye CMOS camera the traffic signs, and provide their automatic recognition on the vehicle network. Differently from the state-of-the-art, in this work color-detection is addressed exploiting the HSI color space which is robust to lighting changes. Hence the first stage of the processing system implements fish-eye correction and RGB to HSI transformation. After color-based detection a noise deletion step is implemented and then, for the classification, a template-based correlation method is adopted to identify potential traffic signs, of different shapes, from acquired images. Starting from a segmented-image a matching with templates of the searched signs is carried out using a distance transform. These templates are organized hierarchically to reduce the number of operations and hence easing real-time processing for several types of traffic signs. Finally, for the recognition of the specific traffic sign, a technique based on extraction of signs characteristics and thresholding is adopted. Implemented on DSP platform the system recognizes traffic signs in less than 150 ms at a distance of about 15 meters from 640x480-pixel acquired images. Tests carried out with hundreds of images show a detection and recognition rate of about 93%.

Study of fish response using particle image velocimetry and high-speed, high-resolution imaging

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

Deng, Z.; Richmond, M. C.; Mueller, R. P.

2004-10-01

Fish swimming has fascinated both engineers and fish biologists for decades. Digital particle image velocimetry (DPIV) and high-speed, high-resolution digital imaging are recently developed analysis tools that can help engineers and biologists better understand how fish respond to turbulent environments. This report details studies to evaluate DPIV. The studies included a review of existing literature on DPIV, preliminary studies to test the feasibility of using DPIV conducted at our Flow Biology Laboratory in Richland, Washington September through December 2003, and applications of high-speed, high-resolution digital imaging with advanced motion analysis to investigations of fish injury mechanisms in turbulent shear flowsmore » and bead trajectories in laboratory physical models. Several conclusions were drawn based on these studies, which are summarized as recommendations for proposed research at the end of this report.« less

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.

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.

Comparative study between quantitative digital image analysis and fluorescence in situ hybridization of breast cancer equivocal human epidermal growth factor receptors 2 score 2(+) cases.

PubMed

Ayad, Essam; Mansy, Mina; Elwi, Dalal; Salem, Mostafa; Salama, Mohamed; Kayser, Klaus

2015-01-01

Optimization of workflow for breast cancer samples with equivocal human epidermal growth factor receptors 2 (HER2)/neu score 2(+) results in routine practice, remains to be a central focus of the on-going efforts to assess HER2 status. According to the College of American Pathologists/American Society of Clinical Oncology guidelines equivocal HER2/neu score 2(+) cases are subject for further testing, usually by fluorescence in situ hybridization (FISH) investigations. It still remains on open question, whether quantitative digital image analysis of HER2 immunohistochemistry (IHC) stained slides can assist in further refining the HER2 score 2(+). To assess utility of quantitative digital analysis of IHC stained slides and compare its performance to FISH in cases of breast cancer with equivocal HER2 score 2(+). Fifteen specimens (previously diagnosed as breast cancer and was evaluated as HER 2(-) score 2(+)) represented the study population. Contemporary new cuts were prepared for re-evaluation of HER2 immunohistochemical studies and FISH examination. All the cases were digitally scanned by iScan (Produced by BioImagene [Now Roche-Ventana]). The IHC signals of HER2 were measured using an automated image analyzing system (MECES, www.Diagnomx.eu/meces). Finally, a comparative study was done between the results of the FISH and the quantitative analysis of the virtual slides. Three out of the 15 cases with equivocal HER2 score 2(+), turned out to be positive (3(+)) by quantitative digital analysis, and 12 were found to be negative in FISH too. Two of these three positive cases proved to be positive with FISH, and only one was negative. Quantitative digital analysis is highly sensitive and relatively specific when compared to FISH in detecting HER2/neu overexpression. Therefore, it represents a potential reliable substitute for FISH in breast cancer cases, which desire further refinement of equivocal IHC results.

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

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.

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

Mineralized rods and cones suggest colour vision in a 300 Myr-old fossil fish.

PubMed

Tanaka, Gengo; Parker, Andrew R; Hasegawa, Yoshikazu; Siveter, David J; Yamamoto, Ryoichi; Miyashita, Kiyoshi; Takahashi, Yuichi; Ito, Shosuke; Wakamatsu, Kazumasa; Mukuda, Takao; Matsuura, Marie; Tomikawa, Ko; Furutani, Masumi; Suzuki, Kayo; Maeda, Haruyoshi

2014-12-23

Vision, which consists of an optical system, receptors and image-processing capacity, has existed for at least 520 Myr. Except for the optical system, as in the calcified lenses of trilobite and ostracod arthropods, other parts of the visual system are not usually preserved in the fossil record, because the soft tissue of the eye and the brain decay rapidly after death, such as within 64 days and 11 days, respectively. The Upper Carboniferous Hamilton Formation (300 Myr) in Kansas, USA, yields exceptionally well-preserved animal fossils in an estuarine depositional setting. Here we show that the original colour, shape and putative presence of eumelanin have been preserved in the acanthodii fish Acanthodes bridgei. We also report on the tissues of its eye, which provides the first record of mineralized rods and cones in a fossil and indicates that this 300 Myr-old fish likely possessed colour vision.

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

Research on marine and freshwater fish identification model based on hyper-spectral imaging technology

NASA Astrophysics Data System (ADS)

Fu, Yan; Guo, Pei-yuan; Xiang, Ling-zi; Bao, Man; Chen, Xing-hai

2013-08-01

With the gradually mature of hyper spectral image technology, the application of the meat nondestructive detection and recognition has become one of the current research focuses. This paper for the study of marine and freshwater fish by the pre-processing and feature extraction of the collected spectral curve data, combined with BP network structure and LVQ network structure, a predictive model of hyper spectral image data of marine and freshwater fish has been initially established and finally realized the qualitative analysis and identification of marine and freshwater fish quality. The results of this study show that hyper spectral imaging technology combined with the BP and LVQ Artificial Neural Network Model can be used for the identification of marine and freshwater fish detection. Hyper-spectral data acquisition can be carried out without any pretreatment of the samples, thus hyper-spectral imaging technique is the lossless, high- accuracy and rapid detection method for quality of fish. In this study, only 30 samples are used for the exploratory qualitative identification of research, although the ideal study results are achieved, we will further increase the sample capacity to take the analysis of quantitative identification and verify the feasibility of this theory.

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.

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

Distant touch hydrodynamic imaging with an artificial lateral line.

PubMed

Yang, Yingchen; Chen, Jack; Engel, Jonathan; Pandya, Saunvit; Chen, Nannan; Tucker, Craig; Coombs, Sheryl; Jones, Douglas L; Liu, Chang

2006-12-12

Nearly all underwater vehicles and surface ships today use sonar and vision for imaging and navigation. However, sonar and vision systems face various limitations, e.g., sonar blind zones, dark or murky environments, etc. Evolved over millions of years, fish use the lateral line, a distributed linear array of flow sensing organs, for underwater hydrodynamic imaging and information extraction. We demonstrate here a proof-of-concept artificial lateral line system. It enables a distant touch hydrodynamic imaging capability to critically augment sonar and vision systems. We show that the artificial lateral line can successfully perform dipole source localization and hydrodynamic wake detection. The development of the artificial lateral line is aimed at fundamentally enhancing human ability to detect, navigate, and survive in the underwater environment.

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.

Robustness of an artificially tailored fisheye imaging system with a curvilinear image surface

NASA Astrophysics Data System (ADS)

Lee, Gil Ju; Nam, Won Il; Song, Young Min

2017-11-01

Curved image sensors inspired by animal and insect eyes have provided a new development direction in next-generation digital cameras. It is known that natural fish eyes afford an extremely wide field of view (FOV) imaging due to the geometrical properties of the spherical lens and hemispherical retina. However, its inherent drawbacks, such as the low off-axis illumination and the fabrication difficulty of a 'dome-like' hemispherical imager, limit the development of bio-inspired wide FOV cameras. Here, a new type of fisheye imaging system is introduced that has simple lens configurations with a curvilinear image surface, while maintaining high off-axis illumination and a wide FOV. Moreover, through comparisons with commercial conventional fisheye designs, it is determined that the volume and required number of optical elements of the proposed design is practical while capturing the fundamental optical performances. Detailed design guidelines for tailoring the proposed optic system are also discussed.

A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

PubMed

Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

2012-01-01

The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

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

The design of a microscopic system for typical fluorescent in-situ hybridization applications

NASA Astrophysics Data System (ADS)

Yi, Dingrong; Xie, Shaochuan

2013-12-01

Fluorescence in situ hybridization (FISH) is a modern molecular biology technique used for the detection of genetic abnormalities in terms of the number and structure of chromosomes and genes. The FISH technique is typically employed for prenatal diagnosis of congenital dementia in the Obstetrics and Genecology department. It is also routinely used to pick up qualifying breast cancer patients that are known to be highly curable by the prescription of Her2 targeted therapy. During the microscopic observation phase, the technician needs to count typically green probe dots and red probe dots contained in a single nucleus and calculate their ratio. This procedure need to be done to over hundreds of nuclei. Successful implementation of FISH tests critically depends on a suitable fluorescent microscope which is primarily imported from overseas due to the complexity of such a system beyond the maturity of the domestic optoelectrical industry. In this paper, the typical requirements of a fluorescent microscope that is suitable for FISH applications are first reviewed. The focus of this paper is on the system design and computational methods of an automatic florescent microscopy with high magnification APO objectives, a fast spinning automatic filter wheel, an automatic shutter, a cooled CCD camera used as a photo-detector, and a software platform for image acquisition, registration, pseudo-color generation, multi-channel fusing and multi-focus fusion. Preliminary results from FISH experiments indicate that this system satisfies routine FISH microscopic observation tasks.

Low-contrast underwater living fish recognition using PCANet

NASA Astrophysics Data System (ADS)

Sun, Xin; Yang, Jianping; Wang, Changgang; Dong, Junyu; Wang, Xinhua

2018-04-01

Quantitative and statistical analysis of ocean creatures is critical to ecological and environmental studies. And living fish recognition is one of the most essential requirements for fishery industry. However, light attenuation and scattering phenomenon are present in the underwater environment, which makes underwater images low-contrast and blurry. This paper tries to design a robust framework for accurate fish recognition. The framework introduces a two stage PCA Network to extract abstract features from fish images. On a real-world fish recognition dataset, we use a linear SVM classifier and set penalty coefficients to conquer data unbalanced issue. Feature visualization results show that our method can avoid the feature distortion in boundary regions of underwater image. Experiments results show that the PCA Network can extract discriminate features and achieve promising recognition accuracy. The framework improves the recognition accuracy of underwater living fishes and can be easily applied to marine fishery industry.

A semi-automated method of monitoring dam passage of American Eels Anguilla rostrata

USGS Publications Warehouse

Welsh, Stuart A.; Aldinger, Joni L.

2014-01-01

Fish passage facilities at dams have become an important focus of fishery management in riverine systems. Given the personnel and travel costs associated with physical monitoring programs, automated or semi-automated systems are an attractive alternative for monitoring fish passage facilities. We designed and tested a semi-automated system for eel ladder monitoring at Millville Dam on the lower Shenandoah River, West Virginia. A motion-activated eel ladder camera (ELC) photographed each yellow-phase American Eel Anguilla rostrata that passed through the ladder. Digital images (with date and time stamps) of American Eels allowed for total daily counts and measurements of eel TL using photogrammetric methods with digital imaging software. We compared physical counts of American Eels with camera-based counts; TLs obtained with a measuring board were compared with TLs derived from photogrammetric methods. Data from the ELC were consistent with data obtained by physical methods, thus supporting the semi-automated camera system as a viable option for monitoring American Eel passage. Time stamps on digital images allowed for the documentation of eel passage time—data that were not obtainable from physical monitoring efforts. The ELC has application to eel ladder facilities but can also be used to monitor dam passage of other taxa, such as crayfishes, lampreys, and water snakes.

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.

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.

Omniview motionless camera orientation system

NASA Technical Reports Server (NTRS)

Martin, H. Lee (Inventor); Kuban, Daniel P. (Inventor); Zimmermann, Steven D. (Inventor); Busko, Nicholas (Inventor)

2010-01-01

An apparatus and method is provided for converting digital images for use in an imaging system. The apparatus includes a data memory which stores digital data representing an image having a circular or spherical field of view such as an image captured by a fish-eye lens, a control input for receiving a signal for selecting a portion of the image, and a converter responsive to the control input for converting digital data corresponding to the selected portion into digital data representing a planar image for subsequent display. Various methods include the steps of storing digital data representing an image having a circular or spherical field of view, selecting a portion of the image, and converting the stored digital data corresponding to the selected portion into digital data representing a planar image for subsequent display. In various embodiments, the data converter and data conversion step may use an orthogonal set of transformation algorithms.

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.

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.

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

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

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.

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.

Cross Matching of VIIRS Boat Detection and Vessel Monitoring System Tracks

NASA Astrophysics Data System (ADS)

Hsu, F. C.; Elvidge, C.; Zhizhin, M. N.; Baugh, K.; Ghosh, T.

2016-12-01

One approach to commercial fishing is to use use bright lights at night to attract catch. This is a widely used practice in East and Southeast Asia, but can also be found in other fisheries. In some cases, the deployed lighting exceeds 100,000 watts. Such lighting is distinctive in dark ocean and can even be seen from space with sensor such as Visible Infrared Imaging Radiometer Suite Day/Night Band (VIIRS-DNB). We have developed a VIIRS Boat Detection (VBD) system, which outputs lists of boat locations in near real time. One of the standard methods fishery agencies use to collect geospatial data on fishing boats is to require boats to carry Vessel Monitoring System beacons. We developed an algorithm to cross-match VBD data with VMS tracks. With this we are able to identify fishing boats that do not carry VMS beacons. In certain situations, this is an indicator of illegal fishing. The other application for this cross-matching is to define the VIIRS detection limits and developing a calibration to estimate deployed wattage. Here we demonstrate results of cross matching VBD and VMS for Indonesia as example to showcase its potential.

Multipurpose spectral imager.

PubMed

Sigernes, F; Lorentzen, D A; Heia, K; Svenøe, T

2000-06-20

A small spectral imaging system is presented that images static or moving objects simultaneously as a function of wavelength. The main physical principle is outlined and demonstrated. The instrument is capable of resolving both spectral and spatial information from targets throughout the entire visible region. The spectral domain has a bandpass of 12 A. One can achieve the spatial domain by rotating the system's front mirror with a high-resolution stepper motor. The spatial resolution range from millimeters to several meters depends mainly on the front optics used and whether the target is fixed (static) or movable relative to the instrument. Different applications and examples are explored, including outdoor landscapes, industrial fish-related targets, and ground-level objects observed in the more traditional way from an airborne carrier (remote sensing). Through the examples, we found that the instrument correctly classifies whether a shrimp is peeled and whether it can disclose the spectral and spatial microcharacteristics of targets such as a fish nematode (parasite). In the macroregime, we were able to distinguish a marine vessel from the surrounding sea and sky. A study of the directional spectral albedo from clouds, mountains, snow cover, and vegetation has also been included. With the airborne experiment, the imager successfully classified snow cover, leads, and new and rafted ice, as seen from 10.000 ft (3.048 m).

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.

Navigation system for a mobile robot with a visual sensor using a fish-eye lens

NASA Astrophysics Data System (ADS)

Kurata, Junichi; Grattan, Kenneth T. V.; Uchiyama, Hironobu

1998-02-01

Various position sensing and navigation systems have been proposed for the autonomous control of mobile robots. Some of these systems have been installed with an omnidirectional visual sensor system that proved very useful in obtaining information on the environment around the mobile robot for position reckoning. In this article, this type of navigation system is discussed. The sensor is composed of one TV camera with a fish-eye lens, using a reference target on a ceiling and hybrid image processing circuits. The position of the robot, with respect to the floor, is calculated by integrating the information obtained from a visual sensor and a gyroscope mounted in the mobile robot, and the use of a simple algorithm based on PTP control for guidance is discussed. An experimental trial showed that the proposed system was both valid and useful for the navigation of an indoor vehicle.

High-resolution frequency domain second harmonic optical coherence tomography

NASA Astrophysics Data System (ADS)

Su, Jianping; Tomov, I. V.; Jiang, Yi; Chen, Zhongping

2007-02-01

We used continuum generated in an 8.5 cm long fiber by a femtosecond Yb fiber laser to improve threefold the axial resolution of frequency domain SH-OCT to 12μm. The acquisition time was shortened by more than two orders of magnitude compared to time domain SH-OCT. The system was applied to image biological tissue of fish scales, pig leg tendon and rabbit eye sclera. Highly organized collagen fibrils can be visualized in the recorded images. Polarization dependence on second harmonic has been used to obtain polarization resolved images.

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.

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.

Gradient Index Optics at DARPA

DTIC Science & Technology

2013-11-01

four efforts were selected for further development and demonstration: fluidic adaptive zoom lenses, foveated imaging, photon sieves, and nanolayer...2-4 1. Fluidic Adaptive Zoom Lenses... gastropod mollusks. In simple optical systems such as the fish lens, the focal length is a function of the wavelength of light. This distortion is called

The Effects of Explicit Visual Cues in Reading Biological Diagrams

ERIC Educational Resources Information Center

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

2017-01-01

Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and…

Effects of the change in cutoff values for human epidermal growth factor receptor 2 status by immunohistochemistry and fluorescence in situ hybridization: a study comparing conventional brightfield microscopy, image analysis-assisted microscopy, and interobserver variation.

PubMed

Atkinson, Roscoe; Mollerup, Jens; Laenkholm, Anne-Vibeke; Verardo, Mark; Hawes, Debra; Commins, Deborah; Engvad, Birte; Correa, Adrian; Ehlers, Charlotte Cort; Nielsen, Kirsten Vang

2011-08-01

New guidelines for HER2 testing have been introduced. To evaluate the difference in HER2 assessment after introduction of new cutoff levels for both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) and to compare interobserver agreement and time to score between image analysis and conventional microscopy. Samples from 150 patients with breast cancer were scored by 7 pathologists using conventional microscopy, with a cutoff of both 10% and 30% IHC-stained cells, and using automated microscopy with image analysis. The IHC results were compared individually and to HER2 status as determined by FISH, using both the approved cutoff of 2.0 and the recently introduced cutoff of 2.2. High concordance was found in IHC scoring among the 7 pathologists. The 30% cutoff led to slightly fewer positive IHC observations. Introduction of a FISH equivocal zone affected 4% of the FISH scores. If cutoff for FISH is kept at 2.0, no difference in patient selection is found between the 10% and the 30% IHC cutoff. Among the 150 breast cancer samples, the new 30% IHC and 2.2 FISH cutoff levels resulted in one case without a firm diagnosis because both IHC and FISH were equivocal. Automated microscopy and image analysis-assisted IHC led to significantly better interobserver agreement among the 7 pathologists, with an increase in mean scoring time of only about 30 seconds per slide. The change in cutoff levels led to a higher concordance between IHC and FISH, but fewer samples were classified as HER2 positive.

Lebanon in the Middle East Subordinate System.

DTIC Science & Technology

1983-06-03

hostility relationship will be borrowed from Kenneth E. Boulding’s pioneering work on "National Images and International systems.ŗ This framework...Quarantine). 3 6 The pioneer American missionary arrived at Beirut in 1823; Pliny Fish, member of the American Board of Commissioners for Foreign...majority in Lebanon’s resident population. Economists and private research institutes conducted research and studies on Lebanese demography . They

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.

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.

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.

DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species.

PubMed

Nwani, Christopher D; Becker, Sven; Braid, Heather E; Ude, Emmanuel F; Okogwu, Okechukwu I; Hanner, Robert

2011-10-01

Fishes are the main animal protein source for human beings and play a vital role in aquatic ecosystems and food webs. Fish identification can be challenging, especially in the tropics (due to high diversity), and this is particularly true for larval forms or fragmentary remains. DNA barcoding, which uses the 5' region of the mitochondrial cytochrome c oxidase subunit I (COI) as a target gene, is an efficient method for standardized species-level identification for biodiversity assessment and conservation, pending the establishment of reference sequence libraries. In this study, fishes were collected from three rivers in southeastern Nigeria, identified morphologically, and imaged digitally. DNA was extracted, PCR-amplified, and the standard barcode region was bidirectionally sequenced for 363 individuals belonging to 70 species in 38 genera. All specimen provenance data and associated sequence information were recorded in the barcode of life data systems (BOLD; www.barcodinglife.org ). Analytical tools on BOLD were used to assess the performance of barcoding to identify species. Using neighbor-joining distance comparison, the average genetic distance was 60-fold higher between species than within species, as pairwise genetic distance estimates averaged 10.29% among congeners and only 0.17% among conspecifics. Despite low levels of divergence within species, we observed river system-specific haplotype partitioning within eight species (11.4% of all species). Our preliminary results suggest that DNA barcoding is very effective for species identification of Nigerian freshwater fishes.

Line-scanning Raman imaging spectroscopy for detection of fingerprints.

PubMed

Deng, Sunan; Liu, Le; Liu, Zhiyi; Shen, Zhiyuan; Li, Guohua; He, Yonghong

2012-06-10

Fingerprints are the best form of personal identification for criminal investigation purposes. We present a line-scanning Raman imaging system and use it to detect fingerprints composed of β-carotene and fish oil on different substrates. Although the line-scanning Raman system has been used to map the distribution of materials such as polystyrene spheres and minerals within geological samples, this is the first time to our knowledge that the method is used in imaging fingerprints. Two Raman peaks of β-carotene (501.2, 510.3 nm) are detected and the results demonstrate that both peaks can generate excellent images with little difference between them. The system operates at a spectra resolution of about 0.4 nm and can detect β-carotene signals in petroleum ether solution with the limit of detection of 3.4×10(-9) mol/L. The results show that the line-scanning Raman imaging spectroscopy we have built has a high accuracy and can be used in the detection of latent fingerprints in the future.

High-resolution frequency-domain second-harmonic optical coherence tomography

NASA Astrophysics Data System (ADS)

Su, Jianping; Tomov, Ivan V.; Jiang, Yi; Chen, Zhongping

2007-04-01

We used continuum generated in an 8.5 cm long fiber by a femtosecond Yb fiber laser to improve threefold the axial resolution of frequency domain second-harmonic optical coherence tomography (SH-OCT) to 12 μm. The acquisition time was shortened by more than 2 orders of magnitude compared to the time-domain SH-OCT. The system was applied to image biological tissue of fish scales, pig leg tendon, and rabbit eye sclera. Highly organized collagen fibrils can be visualized in the recorded images. Polarization dependence on the SH has been used to obtain polarization resolved images.

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.

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.

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.

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.

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

Acoustic water bottom investigation with a remotely operated watercraft survey system

NASA Astrophysics Data System (ADS)

Yamasaki, Shintaro; Tabusa, Tomonori; Iwasaki, Shunsuke; Hiramatsu, Masahiro

2017-12-01

This paper describes a remotely operated investigation system developed by combining a modern leisure-use fish finder and an unmanned watercraft to survey water bottom topography and other data related to bottom materials. Current leisure-use fish finders have strong depth sounding capabilities and can provide precise sonar images and bathymetric information. Because these sonar instruments are lightweight and small, they can be used on unmanned small watercraft. With the developed system, an operator can direct the heading of an unmanned watercraft and monitor a PC display showing real-time positioning information through the use of onboard equipment and long-distance communication devices. Here, we explain how the system was developed and demonstrate the use of the system in an area of submerged woods in a lake. The system is low cost, easy to use, and mobile. It should be useful in surveying areas that have heretofore been hard to investigate, including remote, small, and shallow lakes, for example, volcanic and glacial lakes.

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.

Light-pollution measurement with the Wide-field all-sky image analyzing monitoring system

NASA Astrophysics Data System (ADS)

Vítek, S.

2017-07-01

The purpose of this experiment was to measure light pollution in the capital of Czech Republic, Prague. As a measuring instrument is used calibrated consumer level digital single reflex camera with IR cut filter, therefore, the paper reports results of measuring and monitoring of the light pollution in the wavelength range of 390 - 700 nm, which most affects visual range astronomy. Combining frames of different exposure times made with a digital camera coupled with fish-eye lens allow to create high dynamic range images, contain meaningful values, so such a system can provide absolute values of the sky brightness.

The nonlinear flexural response of a whole teleost fish: Contribution of scales and skin.

PubMed

Szewciw, Lawrence; Zhu, Deju; Barthelat, Francois

2017-12-01

The scaled skin of fish is an intricate system that provides mechanical protection against hard and sharp puncture, while maintaining the high flexural compliance required for unhindered locomotion. This unusual combination of local hardness and global compliance makes fish skin an interesting model for bioinspired protective systems. In this work we investigate the flexural response of whole teleost fish, and how scales may affect global flexural stiffness. A bending moment is imposed on the entire body of a striped bass (Morone saxatilis). Imaging is used to measure local curvature, to generate moment-curvature curves as function of position along the entire axis of the fish. We find that the flexural stiffness is the highest in the thick middle portion of the fish, and lowest in the caudal and rostral ends. The flexural response is nonlinear, with an initial soft response followed by significant stiffening at larger flexural deformations. Low flexural stiffness at low curvatures promotes efficient swimming, while higher stiffness at high curvatures enables a possible tendon effect, where the mechanical energy at the end of a stroke is stored in the form of strain energy in the fish skin. To assess the contribution of the scales to stiffening we performed flexural tests with and without scales, following a careful protocol to take in account tissue degradation and the effects of temperature. Our findings suggest that scales do not substantially increase the whole body flexural stiffness of teleost fish over ranges of deformations which are typical of swimming and maneuvering. Teleost scales are thin and relatively flexible, so they can accommodate large flexural deformations. This finding is in contrast to the bulkier ganoid scales which were shown in previous reports to have a profound impact of global flexural deformations and swimming in fish like gar or Polypterus. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of instream hydraulic and riparian habitat conditions and stream temperatures of the Upper White River Basin, Washington, using multispectral imaging systems

USGS Publications Warehouse

Black, Robert W.; Haggland, Alan; Crosby, Greg

2003-01-01

Instream hydraulic and riparian habitat conditions and stream temperatures were characterized for selected stream segments in the Upper White River Basin, Washington. An aerial multispectral imaging system used digital cameras to photograph the stream segments across multiple wavelengths to characterize fish habitat and temperature conditions. All imageries were georeferenced. Fish habitat features were photographed at a resolution of 0.5 meter and temperature imageries were photographed at a 1.0-meter resolution. The digital multispectral imageries were classified using commercially available software. Aerial photographs were taken on September 21, 1999. Field habitat data were collected from August 23 to October 12, 1999, to evaluate the measurement accuracy and effectiveness of the multispectral imaging in determining the extent of the instream habitat variables. Fish habitat types assessed by this method were the abundance of instream hydraulic features such as pool and riffle habitats, turbulent and non-turbulent habitats, riparian composition, the abundance of large woody debris in the stream and riparian zone, and stream temperatures. Factors such as the abundance of instream woody debris, the location and frequency of pools, and stream temperatures generally are known to have a significant impact on salmon. Instream woody debris creates the habitat complexity necessary to maintain a diverse and healthy salmon population. The abundance of pools is indicative of a stream's ability to support fish and other aquatic organisms. Changes in water temperature can affect aquatic organisms by altering metabolic rates and oxygen requirements, altering their sensitivity to toxic materials and affecting their ability to avoid predators. The specific objectives of this project were to evaluate the use of an aerial multispectral imaging system to accurately identify instream hydraulic features and surface-water temperatures in the Upper White River Basin, to use the multispectral system to help establish baseline instream/riparian habitat conditions in the study area, and to qualitatively assess the imaging system for possible use in other Puget Sound rivers. For the most part, all multispectral imagery-based estimates of total instream riffle and pool area were less than field measurements. The imagery-based estimates for riffle habitat area ranged from 35.5 to 83.3 percent less than field measurements. Pool habitat estimates ranged from 139.3 percent greater than field measurements to 94.0 percent less than field measurements. Multispectral imagery-based estimates of turbulent habitat conditions ranged from 9.3 percent greater than field measurements to 81.6 percent less than field measurements. Multispectral imagery-based estimates of non-turbulent habitat conditions ranged from 27.7 to 74.1 percent less than field measurements. The absolute average percentage of difference between field and imagery-based habitat type areas was less for the turbulent and non-turbulent habitat type categories than for pools and riffles. The estimate of woody debris by multispectral imaging was substantially different than field measurements; percentage of differences ranged from +373.1 to -100 percent. Although the total area of riffles, pools, and turbulent and non-turbulent habitat types measured in the field were all substantially higher than those estimated from the multispectral imagery, the percentage of composition of each habitat type was not substantially different between the imagery-based estimates and field measurements.

Application of the airborne ocean color imager for commercial fishing

NASA Technical Reports Server (NTRS)

Wrigley, Robert C.

1993-01-01

The objective of the investigation was to develop a commercial remote sensing system for providing near-real-time data (within one day) in support of commercial fishing operations. The Airborne Ocean Color Imager (AOCI) had been built for NASA by Daedalus Enterprises, Inc., but it needed certain improvements, data processing software, and a delivery system to make it into a commercial system for fisheries. Two products were developed to support this effort: the AOCI with its associated processing system and an information service for both commercial and recreational fisheries to be created by Spectro Scan, Inc. The investigation achieved all technical objectives: improving the AOCI, creating software for atmospheric correction and bio-optical output products, georeferencing the output products, and creating a delivery system to get those products into the hands of commercial and recreational fishermen in near-real-time. The first set of business objectives involved Daedalus Enterprises and also were achieved: they have an improved AOCI and new data processing software with a set of example data products for fisheries applications to show their customers. Daedalus' marketing activities showed the need for simplification of the product for fisheries, but they successfully marketed the current version to an Italian consortium. The second set of business objectives tasked Spectro Scan to provide an information service and they could not be achieved because Spectro Scan was unable to obtain necessary venture capital to start up operations.

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.

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.

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...

Calcium neuroimaging in behaving zebrafish larvae using a turn-key light field camera

NASA Astrophysics Data System (ADS)

Cruz Perez, Carlos; Lauri, Antonella; Symvoulidis, Panagiotis; Cappetta, Michele; Erdmann, Arne; Westmeyer, Gil Gregor

2015-09-01

Reconstructing a three-dimensional scene from multiple simultaneously acquired perspectives (the light field) is an elegant scanless imaging concept that can exceed the temporal resolution of currently available scanning-based imaging methods for capturing fast cellular processes. We tested the performance of commercially available light field cameras on a fluorescent microscopy setup for monitoring calcium activity in the brain of awake and behaving reporter zebrafish larvae. The plenoptic imaging system could volumetrically resolve diverse neuronal response profiles throughout the zebrafish brain upon stimulation with an aversive odorant. Behavioral responses of the reporter fish could be captured simultaneously together with depth-resolved neuronal activity. Overall, our assessment showed that with some optimizations for fluorescence microscopy applications, commercial light field cameras have the potential of becoming an attractive alternative to custom-built systems to accelerate molecular imaging research on cellular dynamics.

Calcium neuroimaging in behaving zebrafish larvae using a turn-key light field camera.

PubMed

Perez, Carlos Cruz; Lauri, Antonella; Symvoulidis, Panagiotis; Cappetta, Michele; Erdmann, Arne; Westmeyer, Gil Gregor

2015-09-01

Reconstructing a three-dimensional scene from multiple simultaneously acquired perspectives (the light field) is an elegant scanless imaging concept that can exceed the temporal resolution of currently available scanning-based imaging methods for capturing fast cellular processes. We tested the performance of commercially available light field cameras on a fluorescent microscopy setup for monitoring calcium activity in the brain of awake and behaving reporter zebrafish larvae. The plenoptic imaging system could volumetrically resolve diverse neuronal response profiles throughout the zebrafish brain upon stimulation with an aversive odorant. Behavioral responses of the reporter fish could be captured simultaneously together with depth-resolved neuronal activity. Overall, our assessment showed that with some optimizations for fluorescence microscopy applications, commercial light field cameras have the potential of becoming an attractive alternative to custom-built systems to accelerate molecular imaging research on cellular dynamics.

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.

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.

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

Application of ERTS-1 imagery to the harvest model of the US Menhaden fishery

NASA Technical Reports Server (NTRS)

Maughan, P. M.; Marmelstein, A. D.; Temple, O. R.

1973-01-01

Preliminary results of an experiment to demonstrate the utility of ERTS-1 imagery for providing significant information to the harvest model of the menhaden industry are reported. Fisheries and related environmental data were obtained discontinuously throughout the 1973 menhaden (a surface schooling, coastal species) fishing season in Mississippi Sound. The unexpected complexity of the physical environment in Mississippi Sound precluded simplistic analysis of fish/environment relationships. Preliminary indications are that an association does exist between fish availability and differences in water transparency (turbidity) within the Sound. A clearer relationship is developing between major turbid features, imaged by ERTS-1 and location of successful fishing attempts. On all occasions where relatively cloudfree ERTS-1 overflight days coincided with fishery activity, overlays of catch location of ERTS-1 images show an association of school position with interfaces between imaged turbid features. Analysis is currently underway to determine persistence of such associations in an attempt to define minimum satellite return time necessary to maintain continuity of associations.

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.

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

Small real time detection satellites for MDA using hyperspectral imaging

NASA Astrophysics Data System (ADS)

Nakaya, Daiki; Yanagida, Hiroki; Shin, Satori; Ito, Tomonori; Takeuchi, Yusuke

2017-10-01

Hyperspectral Images are now used in the field of agriculture, cosmetics, and space exploring. Behind this fact, there is a result of efforts to contrive miniaturization and decrease in costs. This paper describes low-cost and small Hyperspectral Camera (HSC) under development and a method of utilizing it. Real Time Detection System for MDA is that government agencies put those cameras in small satellites and use them for MDA (Maritime Domain Awareness). We assume early detection of unidentified floating objects to find out disguised fishing ships and submarines.

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®

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.

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.

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.

Early evolution of multifocal optics for well-focused colour vision in vertebrates.

PubMed

Gustafsson, O S E; Collin, S P; Kröger, R H H

2008-05-01

Jawless fishes (Agnatha; lampreys and hagfishes) most closely resemble the earliest stage in vertebrate evolution and lamprey-like animals already existed in the Lower Cambrian [about 540 million years ago (MYA)]. Agnathans are thought to have separated from the main vertebrate lineage at least 500 MYA. Hagfishes have primitive eyes, but the eyes of adult lampreys are well-developed. The southern hemisphere lamprey, Geotria australis, possesses five types of opsin genes, three of which are clearly orthologous to the opsin genes of jawed vertebrates. This suggests that the last common ancestor of all vertebrate lineages possessed a complex colour vision system. In the eyes of many bony fishes and tetrapods, well-focused colour images are created by multifocal crystalline lenses that compensate for longitudinal chromatic aberration. To trace the evolutionary origins of multifocal lenses, we studied the optical properties of the lenses in four species of lamprey (Geotria australis, Mordacia praecox, Lampetra fluviatilis and Petromyzon marinus), with representatives from all three of the extant lamprey families. Multifocal lenses are present in all lampreys studied. This suggests that the ability to create well-focused colour images with multifocal optical systems also evolved very early.

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH.

PubMed

Bolková, Jitka; Lanctôt, Christian

2016-04-01

Advances in fluorescent probe design and synthesis have allowed the uniform in situ labeling of individual RNA molecules. In a technique referred to as single molecule RNA FISH (smRNA FISH), the labeled RNA molecules can be imaged as diffraction-limited spots and counted using image analysis algorithms. Single RNA counting has provided valuable insights into the process of gene regulation. This microscopy-based method has often revealed a high cell-to-cell variability in expression levels, which has in turn led to a growing interest in investigating the biological significance of gene expression noise. Here we describe the application of the smRNA FISH technique to samples of Caenorhabditis elegans, a well-characterized model organism. Copyright © 2015 Elsevier Inc. 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

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.

Performance benefits and limitations of a camera network

NASA Astrophysics Data System (ADS)

Carr, Peter; Thomas, Paul J.; Hornsey, Richard

2005-06-01

Visual information is of vital significance to both animals and artificial systems. The majority of mammals rely on two images, each with a resolution of 107-108 'pixels' per image. At the other extreme are insect eyes where the field of view is segmented into 103-105 images, each comprising effectively one pixel/image. The great majority of artificial imaging systems lie nearer to the mammalian characteristics in this parameter space, although electronic compound eyes have been developed in this laboratory and elsewhere. If the definition of a vision system is expanded to include networks or swarms of sensor elements, then schools of fish, flocks of birds and ant or termite colonies occupy a region where the number of images and the pixels/image may be comparable. A useful system might then have 105 imagers, each with about 104-105 pixels. Artificial analogs to these situations include sensor webs, smart dust and co-ordinated robot clusters. As an extreme example, we might consider the collective vision system represented by the imminent existence of ~109 cellular telephones, each with a one-megapixel camera. Unoccupied regions in this resolution-segmentation parameter space suggest opportunities for innovative artificial sensor network systems. Essential for the full exploitation of these opportunities is the availability of custom CMOS image sensor chips whose characteristics can be tailored to the application. Key attributes of such a chip set might include integrated image processing and control, low cost, and low power. This paper compares selected experimentally determined system specifications for an inward-looking array of 12 cameras with the aid of a camera-network model developed to explore the tradeoff between camera resolution and the number of cameras.

Volumetric flow around a swimming lamprey

NASA Astrophysics Data System (ADS)

Lehn, Andrea M.; Colin, Sean P.; Costello, John H.; Leftwich, Megan C.; Tytell, Eric D.

2015-11-01

A primary experimental technique for studying fluid-structure interactions around swimming fish has been planar dimensional particle image velocimetry (PIV). Typically, two components of the velocity vector are measured in a plane, in the case of swimming studies, directly behind the animal. While useful, this approach provides little to no insight about fluid structure interactions above and below the fish. For fish with a small height relative to body length, such as the long and approximately cylindrical lamprey, 3D information is essential to characterize how these fish interact with their fluid environment. This study presents 3D flow structures along the body and in the wake of larval lamprey, P etromyzon m arinus , which are 10-15 cm long. Lamprey swim through a 1000 cm3 field of view in a standard 10 gallon tank illuminated by a green laser. Data are collected using the three component velocimeter V3V system by TSI, Inc. and processed using Insight 4G software. This study expands on previous works that show two pairs of vortices each tail beat in the mid-plane of the lamprey wake. NSF DMS 1062052.

Fish swarm intelligent to optimize real time monitoring of chips drying using machine vision

NASA Astrophysics Data System (ADS)

Hendrawan, Y.; Hawa, L. C.; Damayanti, R.

2018-03-01

This study attempted to apply machine vision-based chips drying monitoring system which is able to optimise the drying process of cassava chips. The objective of this study is to propose fish swarm intelligent (FSI) optimization algorithms to find the most significant set of image features suitable for predicting water content of cassava chips during drying process using artificial neural network model (ANN). Feature selection entails choosing the feature subset that maximizes the prediction accuracy of ANN. Multi-Objective Optimization (MOO) was used in this study which consisted of prediction accuracy maximization and feature-subset size minimization. The results showed that the best feature subset i.e. grey mean, L(Lab) Mean, a(Lab) energy, red entropy, hue contrast, and grey homogeneity. The best feature subset has been tested successfully in ANN model to describe the relationship between image features and water content of cassava chips during drying process with R2 of real and predicted data was equal to 0.9.

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.

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

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.

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.

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

Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy

PubMed Central

Quirin, Sean; Vladimirov, Nikita; Yang, Chao-Tsung; Peterka, Darcy S.; Yuste, Rafael; Ahrens, Misha B.

2016-01-01

Increasing the volumetric imaging speed of light-sheet microscopy will improve its ability to detect fast changes in neural activity. Here, a system is introduced for brain-wide imaging of neural activity in the larval zebrafish by coupling structured illumination with cubic phase extended depth-of-field (EDoF) pupil encoding. This microscope enables faster light-sheet imaging and facilitates arbitrary plane scanning—removing constraints on acquisition speed, alignment tolerances, and physical motion near the sample. The usefulness of this method is demonstrated by performing multi-plane calcium imaging in the fish brain with a 416 × 832 × 160 µm field of view at 33 Hz. The optomotor response behavior of the zebrafish is monitored at high speeds, and time-locked correlations of neuronal activity are resolved across its brain. PMID:26974063

Enhanced optical design by distortion control

NASA Astrophysics Data System (ADS)

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

2005-09-01

The control of optical distortion is useful for the design of a variety of optical system. The most popular is the F-theta lens used in laser scanning system to produce a constant scan velocity across the image plane. Many authors have designed during the last 20 years distortion control corrector. Today, many challenging digital imaging system can use distortion the enhanced their imaging capability. A well know example is a reversed telephoto type, if the barrel distortion is increased instead of being corrected; the result is a so-called Fish-eye lens. However, if we control the barrel distortion instead of only increasing it, the resulting system can have enhanced imaging capability. This paper will present some lens design and real system examples that clearly demonstrate how the distortion control can improve the system performances such as resolution. We present innovative optical system which increases the resolution in the field of view of interest to meet the needs of specific applications. One critical issue when we designed using distortion is the optimization management. Like most challenging lens design, the automatic optimization is less reliable. Proper management keeps the lens design within the correct range, which is critical for optimal performance (size, cost, manufacturability). Many lens design presented tailor a custom merit function and approach.

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

Composition, Distribution and Abundance of Anthropogenic Marine Debris in Northwest Atlantic Submarine Canyons

NASA Astrophysics Data System (ADS)

Heyl, T. P.; Nizinski, M. S.; Kinlan, B. P.; Shank, T. M.

2016-02-01

Submarine canyons are important productive habitats in the deep-sea, as well as downslope conduits for transporting sediment and organic material that enhances local and regional species diversity, including species and ecosystems vulnerable to anthropogenic activities. In 2012 and 2013, we documented and characterized deep-sea coral and sponge ecosystems in virtually unexplored northeast and mid-Atlantic canyons using WHOI's TowCam towed imaging system on the FSV Bigelow. Specifically, thirty-eight digital image TowCam surveys were completed in 10 canyons, with more than 91,000 images documenting not only deep-sea coral and sponge ecosystems and habitat features, but also anthropogenic debris. Canyons surveyed cover most of the latitudinal range of the northeast US region and include Toms Canyon complex, Ryan, Veatch, Gilbert, Powell, and Munson canyons. Each of these canyon hosted debris across depths of 550 to 2100m, consisting mostly of fisheries equipment, including fishing lines, traps, and nets. Potentially-land-based debris (e.g., plastic bags and magazines) was also present in all canyons surveyed. These substrates likely enhance colonization and often served as habitat for specific sessile and mobile species. Comparisons of debris in these canyons revealed depth-related differences, likely due to offshore extent of fishing activities, and will be compared to density and abundances of other deep-sea environments. The occurrence of anthropogenic debris on Northeast US canyon floors suggests major sources via transport ship and fishing-related activities and perhaps the rapid transport of debris through near-shore zones and entrainment in bottom currents.

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

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.

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;

Coloring the Sea Around the Pribilof Islands

NASA Image and Video Library

2017-12-08

The Operational Land Imager (OLI) on Landsat 8 captured this view of a phytoplankton bloom near Alaska’s Pribilof Islands on Sept. 22, 2014. The Pribilofs are surrounded by nutrient-rich waters in the Bering Sea. The milky green and light blue shading of the water indicates the presence of vast populations of microscopic phytoplankton—mostly coccolithophores, which have calcite scales that appear white in satellite images. Such phytoplankton form the foundation of a tremendously productive habitat for fish and birds. Blooms in the Bering Sea increase significantly in springtime, after winter ice cover retreats and nutrients and freshened water are abundant near the ocean surface. Phytoplankton populations plummet in summertime as the water warms, surface nutrients are depleted by blooms, and the plant-like organisms are depleted by grazing fish, zooplankton, and other marine life. By autumn, storms can stir nutrients back to the surface and cooler waters make better bloom conditions. More information: earthobservatory.nasa.gov/IOTD/view.php?id=85043&eocn... Image Credit: NASA/Landsat 8 NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Measuring high-resolution sky luminance distributions with a CCD camera.

PubMed

Tohsing, Korntip; Schrempf, Michael; Riechelmann, Stefan; Schilke, Holger; Seckmeyer, Gunther

2013-03-10

We describe how sky luminance can be derived from a newly developed hemispherical sky imager (HSI) system. The system contains a commercial compact charge coupled device (CCD) camera equipped with a fish-eye lens. The projection of the camera system has been found to be nearly equidistant. The luminance from the high dynamic range images has been calculated and then validated with luminance data measured by a CCD array spectroradiometer. The deviation between both datasets is less than 10% for cloudless and completely overcast skies, and differs by no more than 20% for all sky conditions. The global illuminance derived from the HSI pictures deviates by less than 5% and 20% under cloudless and cloudy skies for solar zenith angles less than 80°, respectively. This system is therefore capable of measuring sky luminance with the high spatial and temporal resolution of more than a million pixels and every 20 s respectively.

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.

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.

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

Advances in photon counting for bioluminescence

NASA Astrophysics Data System (ADS)

Ingle, Martin B.; Powell, Ralph

1998-11-01

Photon counting systems were originally developed for astronomy, initially by the astronomical community. However, a major application area is in the study of luminescent probes in living plants, fishes and cell cultures. For these applications, it has been necessary to develop camera system capability at very low light levels -- a few photons occasionally -- and also at reasonably high light levels to enable the systems to be focused and to collect quality images of the object under study. The paper presents new data on MTF at extremely low photon flux and conventional ICCD illumination, counting efficiency and dark noise as a function of temperature.

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

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.

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.

Researches on hazard avoidance cameras calibration of Lunar Rover

NASA Astrophysics Data System (ADS)

Li, Chunyan; Wang, Li; Lu, Xin; Chen, Jihua; Fan, Shenghong

2017-11-01

Lunar Lander and Rover of China will be launched in 2013. It will finish the mission targets of lunar soft landing and patrol exploration. Lunar Rover has forward facing stereo camera pair (Hazcams) for hazard avoidance. Hazcams calibration is essential for stereo vision. The Hazcam optics are f-theta fish-eye lenses with a 120°×120° horizontal/vertical field of view (FOV) and a 170° diagonal FOV. They introduce significant distortion in images and the acquired images are quite warped, which makes conventional camera calibration algorithms no longer work well. A photogrammetric calibration method of geometric model for the type of optical fish-eye constructions is investigated in this paper. In the method, Hazcams model is represented by collinearity equations with interior orientation and exterior orientation parameters [1] [2]. For high-precision applications, the accurate calibration model is formulated with the radial symmetric distortion and the decentering distortion as well as parameters to model affinity and shear based on the fisheye deformation model [3] [4]. The proposed method has been applied to the stereo camera calibration system for Lunar Rover.

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

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.

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.

Automatic electronic fish tracking system

NASA Technical Reports Server (NTRS)

Osborne, P. W.; Hoffman, E.; Merriner, J. V.; Richards, C. E.; Lovelady, R. W.

1976-01-01

A newly developed electronic fish tracking system to automatically monitor the movements and migratory habits of fish is reported. The system is aimed particularly at studies of effects on fish life of industrial facilities which use rivers or lakes to dump their effluents. Location of fish is acquired by means of acoustic links from the fish to underwater Listening Stations, and by radio links which relay tracking information to a shore-based Data Base. Fish over 4 inches long may be tracked over a 5 x 5 mile area. The electronic fish tracking system provides the marine scientist with electronics which permit studies that were not practical in the past and which are cost-effective compared to manual methods.

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.

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.

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

oRis: multiagents approach for image processing

NASA Astrophysics Data System (ADS)

Rodin, Vincent; Harrouet, Fabrice; Ballet, Pascal; Tisseau, Jacques

1998-09-01

In this article, we present a parallel image processing system based on the concept of reactive agents. This means that, in our system, each agent has a very simple behavior which allows it to take a decision (find out an edge, a region, ...) according to its position in the image and to the information enclosed in it. Our system lies in the oRis language, which allows to describe very finely and simply the agents' behaviors. In fact, oRis is an interpreted and dynamic multiagent language. First of all, oRis is an object language with the use of classes regrouping attributes and methods. The syntax is close to the C++ language and includes notions of multiple inheritance, oRis is also an agent language: every object with a method `main()' becomes an agent. This method is cyclically executed by the system scheduler and corresponds to the agent behavior. We also present an application made with oRis. This application allows to detect concentric striae located on different natural `objects' (age-rings of tree, fish otolith growth rings, striae of some minerals, ...). The stopping of the multiagent system is implemented through a technique issued from immunology: the apoptosis.

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.

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.

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.

The effects of explicit visual cues in reading biological diagrams

NASA Astrophysics Data System (ADS)

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

2017-03-01

Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and energy pyramid, were selected as the reading materials for the control group and reformatted in tree structure or with additional arrows as the diagrams for the treatment group. A quasi-experiment with an online reading test was conducted to examine the effect of the different image conditions on reading comprehension of the two groups. In total, 192 Taiwanese participants from year 7 were assigned randomly into either control group or treatment group according to the pre-test of relevant prior knowledge. The results indicated that not all explicit visual cues were significantly efficient. Only the explicit tree-structured diagrams cued significantly the key concepts of qualitative class-inclusion, parallel relations, and fish taxonomy. Meanwhile the effect of indexical arrows was not significant. The inconsistent effect of tree structure and arrows might be related to the extent of image reformation in which the tree-structured diagrams had undergone radical change of knowledge representation; meanwhile, the arrows had not changed the diagram structure of energy pyramid. The factor of prior knowledge was essential in considering the influence of image design as the effect of diagrams was very different for low and high prior knowledge students. Implications are drawn for the importance of visual design in textbooks.

Flapping propulsion with side-by-side pitching foils

NASA Astrophysics Data System (ADS)

Huera-Huarte, Francisco

2016-11-01

Fish schools are one of the most common types of collective behaviour observed in nature. One of the reasons why fish swim in groups, is to reduce the cost of transport of the school. In this work we explore the propulsive performance of two foils flapping in a symmetric configuration, i.e. with an out-of-phase flapping motion. Direct thrust measurements and Particle Image Velocimetry (PIV) allowed a detailed examination of the forces and the wake generated by the system, for different kinematics (swept angles and frequencies) and shaft separations. For certain specific cases, volumetric PIV shows major differences on how the different structures in the wake of the system evolve, depending on the imposed kinematics and the side-by-side separation between the foils. Results obtained will be compared against data produced with isolated flapping foils with similar imposed kinematics, with the aim to better understand the interactions between both and the performance of the system as a whole. The author would like to acknowledge the financial support provided by the Spanish Ministerio de Economia y competitividad (MINECO) through Grant DPI2015-71645-P.

Three-Dimensional Stratification of Bacterial Biofilm Populations in a Moving Bed Biofilm Reactor for Nitritation-Anammox

PubMed Central

Almstrand, Robert; Persson, Frank; Daims, Holger; Ekenberg, Maria; Christensson, Magnus; Wilén, Britt-Marie; Sörensson, Fred; Hermansson, Malte

2014-01-01

Moving bed biofilm reactors (MBBRs) are increasingly used for nitrogen removal with nitritation-anaerobic ammonium oxidation (anammox) processes in wastewater treatment. Carriers provide protected surfaces where ammonia oxidizing bacteria (AOB) and anammox bacteria form complex biofilms. However, the knowledge about the organization of microbial communities in MBBR biofilms is sparse. We used new cryosectioning and imaging methods for fluorescence in situ hybridization (FISH) to study the structure of biofilms retrieved from carriers in a nitritation-anammox MBBR. The dimensions of the carrier compartments and the biofilm cryosections after FISH showed good correlation, indicating little disturbance of biofilm samples by the treatment. FISH showed that Nitrosomonas europaea/eutropha-related cells dominated the AOB and Candidatus Brocadia fulgida-related cells dominated the anammox guild. New carriers were initially colonized by AOB, followed by anammox bacteria proliferating in the deeper biofilm layers, probably in anaerobic microhabitats created by AOB activity. Mature biofilms showed a pronounced three-dimensional stratification where AOB dominated closer to the biofilm-water interface, whereas anammox were dominant deeper into the carrier space and towards the walls. Our results suggest that current mathematical models may be oversimplifying these three-dimensional systems and unless the multidimensionality of these systems is considered, models may result in suboptimal design of MBBR carriers. PMID:24481066

A simple automated system for appetitive conditioning of zebrafish in their home tanks.

PubMed

Doyle, Jillian M; Merovitch, Neil; Wyeth, Russell C; Stoyek, Matthew R; Schmidt, Michael; Wilfart, Florentin; Fine, Alan; Croll, Roger P

2017-01-15

We describe here an automated apparatus that permits rapid conditioning paradigms for zebrafish. Arduino microprocessors were used to control the delivery of auditory or visual stimuli to groups of adult or juvenile zebrafish in their home tanks in a conventional zebrafish facility. An automatic feeder dispensed precise amounts of food immediately after the conditioned stimuli, or at variable delays for controls. Responses were recorded using inexpensive cameras, with the video sequences analysed with ImageJ or Matlab. Fish showed significant conditioned responses in as few as 5 trials, learning that the conditioned stimulus was a predictor of food presentation at the water surface and at the end of the tank where the food was dispensed. Memories of these conditioned associations persisted for at least 2days after training when fish were tested either as groups or as individuals. Control fish, for which the auditory or visual stimuli were specifically unpaired with food, showed no comparable responses. This simple, low-cost, automated system permits scalable conditioning of zebrafish with minimal human intervention, greatly reducing both variability and labour-intensiveness. It will be useful for studies of the neural basis of learning and memory, and for high-throughput screening of compounds modifying those processes. Copyright © 2016 Elsevier B.V. All rights reserved.

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

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.

Photogrammetry System and Method for Determining Relative Motion Between Two Bodies

NASA Technical Reports Server (NTRS)

Miller, Samuel A. (Inventor); Severance, Kurt (Inventor)

2014-01-01

A photogrammetry system and method provide for determining the relative position between two objects. The system utilizes one or more imaging devices, such as high speed cameras, that are mounted on a first body, and three or more photogrammetry targets of a known location on a second body. The system and method can be utilized with cameras having fish-eye, hyperbolic, omnidirectional, or other lenses. The system and method do not require overlapping fields-of-view if two or more cameras are utilized. The system and method derive relative orientation by equally weighting information from an arbitrary number of heterogeneous cameras, all with non-overlapping fields-of-view. Furthermore, the system can make the measurements with arbitrary wide-angle lenses on the cameras.

Ergonomic approaches to designing educational materials for immersive multi-projection system

NASA Astrophysics Data System (ADS)

Shibata, Takashi; Lee, JaeLin; Inoue, Tetsuri

2014-02-01

Rapid advances in computer and display technologies have made it possible to present high quality virtual reality (VR) environment. To use such virtual environments effectively, research should be performed into how users perceive and react to virtual environment in view of particular human factors. We created a VR simulation of sea fish for science education, and we conducted an experiment to examine how observers perceive the size and depth of an object within their reach and evaluated their visual fatigue. We chose a multi-projection system for presenting the educational VR simulation, because this system can provide actual-size objects and produce stereo images located close to the observer. The results of the experiment show that estimation of size and depth was relatively accurate when subjects used physical actions to assess them. Presenting images within the observer's reach is suggested to be useful for education in VR environment. Evaluation of visual fatigue shows that the level of symptoms from viewing stereo images with a large disparity in VR environment was low in a short time.

PNNL Tests Fish Passage System

ScienceCinema

Colotelo, Alison

2018-01-16

Scientists from PNNL are testing a fish transportation system developed by Whooshh Innovations. The Whooshh system uses a flexible tube that works a bit like a vacuum, guiding fish over hydroelectric dams or other structures. Compared to methods used today, this system could save money while granting fish quicker, safer passage through dams and hatcheries.

PNNL Tests Fish Passage System

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

Colotelo, Alison

2015-03-13

Scientists from PNNL are testing a fish transportation system developed by Whooshh Innovations. The Whooshh system uses a flexible tube that works a bit like a vacuum, guiding fish over hydroelectric dams or other structures. Compared to methods used today, this system could save money while granting fish quicker, safer passage through dams and hatcheries.

A portable freshwater closed-system fish egg incubation system

USGS Publications Warehouse

Sutherland, Jenny L.; Manny, Bruce A.; Kennedy, Gregory W.; Roseman, Edward F.; Allen, Jeffrey D.; Black, M. Glen

2014-01-01

To identify fish eggs collected in the field to species, a portable closed-system fish egg incubation system was designed and used to incubate and hatch the eggs in the laboratory. The system is portable, small in scale (2.54 × 1.52 × 2.03 m), and affordable, with the approximate cost of the system being US$8,300 (2012). The main tank is 678 L and holds a battery of up to 21 (egg) incubation jars. The system includes three independent water pumping systems to (1) provide aerated water to hatching jars, (2) filter and sterilize incubation water, and (3) provide temperature-controlled water in the main tank bath and the incubation jars. The system was successfully used to incubate freshwater fish eggs to raise resulting larvae to the post-yolk-sac stage for three seasons (spring 2012, spring 2013, and fall 2013) over two consecutive years, at two different locations, enabling us to identify fish eggs to species by providing identifiable fish larvae from incubated fish eggs.

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.

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

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.

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).

Single cell systems biology by super-resolution imaging and combinatorial labeling

PubMed Central

Lubeck, Eric; Cai, Long

2012-01-01

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using Fluorescence in situ Hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells provides a natural approach to bring systems biology into single cells. PMID:22660740

Anisakid larva parasitizing Plagioscion squamosissimus in Marajó Bay and Tapajós River, state of Pará, Brazil.

PubMed

Fontenelle, Gabrielle; Knoff, Marcelo; Felizardo, Nilza Nunes; Torres, Eduardo José Lopes; Matos, Edilson Rodrigues; Gomes, Delir Corrêa; São Clemente, Sérgio Carmona de

2016-01-01

In November 2014 and May 2015, a total of 44 specimens of the South American silver croaker Plagioscion squamosissimus were collected: 30 in Marajó Bay and 14 in the Tapajós River, state of Pará, Brazil. The aim was to investigate the presence of anisakid nematodes and determine their parasitism indices and sites of infection, because of their importance regarding health inspection. Sixty-nine Anisakis sp. larvae were found; among them, 16 larvae in seven fish collected in Marajó Bay and 53 larvae in four fish in the Tapajós River. The parasitism indices of the nematodes collected from the fish in Marajó Bay comprised prevalence (P) of 23%, mean infection intensity (MI) of 2.28, mean abundance (MA) of 0.53, range of infection (RI) of 1-4, and infection site (IS) in the mesentery. The fish from the Tapajós River showed P = 28%, MI = 13.2, MA = 3.8, RI = 1-22, and IS = mesentery and intestine. To assist in taxonomic identification, images of the specimens obtained through optical microscopy with Nomarski's interferential contrast system and scanning electron microscopy were used. This is the first record of Anisakis sp. parasitizing P. squamosissimus.

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...

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.

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.

Using video playbacks to study visual communication in a marine fish, Salaria pavo.

PubMed

Gonçalves; Oliveira; Körner; Poschadel; Schlupp

2000-09-01

Video playbacks have been successfully applied to the study of visual communication in several groups of animals. However, this technique is controversial as video monitors are designed with the human visual system in mind. Differences between the visual capabilities of humans and other animals will lead to perceptually different interpretations of video images. We simultaneously presented males and females of the peacock blenny, Salaria pavo, with a live conspecific male and an online video image of the same individual. Video images failed to elicit appropriate responses. Males were aggressive towards the live male but not towards video images of the same male. Similarly, females courted only the live male and spent more time near this stimulus. In contrast, females of the gynogenetic poecilid Poecilia formosa showed an equal preference for a live and video image of a P. mexicana male, suggesting a response to live animals as strong as to video images. We discuss differences between the species that may explain their opposite reaction to video images. Copyright 2000 The Association for the Study of Animal Behaviour.

Star-Mapping Tools Enable Tracking of Endangered Animals

NASA Technical Reports Server (NTRS)

2009-01-01

Software programmer Jason Holmberg of Portland, Oregon, partnered with a Goddard Space Flight Center astrophysicist to develop a method for tracking the elusive whale shark using the unique spot patterns on the fish s skin. Employing a star-mapping algorithm originally designed for the Hubble Space Telescope, Holmberg created the Shepherd Project, a photograph database and pattern-matching system that can identify whale sharks by their spots and match images contributed to the database by photographers from around the world. The system has been adapted for tracking other rare and endangered animals, including polar bears and ocean sunfish.

Imaging Subcellular Structures in the Living Zebrafish Embryo.

PubMed

Engerer, Peter; Plucinska, Gabriela; Thong, Rachel; Trovò, Laura; Paquet, Dominik; Godinho, Leanne

2016-04-02

In vivo imaging provides unprecedented access to the dynamic behavior of cellular and subcellular structures in their natural context. Performing such imaging experiments in higher vertebrates such as mammals generally requires surgical access to the system under study. The optical accessibility of embryonic and larval zebrafish allows such invasive procedures to be circumvented and permits imaging in the intact organism. Indeed the zebrafish is now a well-established model to visualize dynamic cellular behaviors using in vivo microscopy in a wide range of developmental contexts from proliferation to migration and differentiation. A more recent development is the increasing use of zebrafish to study subcellular events including mitochondrial trafficking and centrosome dynamics. The relative ease with which these subcellular structures can be genetically labeled by fluorescent proteins and the use of light microscopy techniques to image them is transforming the zebrafish into an in vivo model of cell biology. Here we describe methods to generate genetic constructs that fluorescently label organelles, highlighting mitochondria and centrosomes as specific examples. We use the bipartite Gal4-UAS system in multiple configurations to restrict expression to specific cell-types and provide protocols to generate transiently expressing and stable transgenic fish. Finally, we provide guidelines for choosing light microscopy methods that are most suitable for imaging subcellular dynamics.

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.

Strategies for rare-event detection: an approach for automated fetal cell detection in maternal blood.

PubMed Central

Oosterwijk, J C; Knepflé, C F; Mesker, W E; Vrolijk, H; Sloos, W C; Pattenier, H; Ravkin, I; van Ommen, G J; Kanhai, H H; Tanke, H J

1998-01-01

This article explores the feasibility of the use of automated microscopy and image analysis to detect the presence of rare fetal nucleated red blood cells (NRBCs) circulating in maternal blood. The rationales for enrichment and for automated image analysis for "rare-event" detection are reviewed. We also describe the application of automated image analysis to 42 maternal blood samples, using a protocol consisting of one-step enrichment followed by immunocytochemical staining for fetal hemoglobin (HbF) and FISH for X- and Y-chromosomal sequences. Automated image analysis consisted of multimode microscopy and subsequent visual evaluation of image memories containing the selected objects. The FISH results were compared with the results of conventional karyotyping of the chorionic villi. By use of manual screening, 43% of the slides were found to be positive (>=1 NRBC), with a mean number of 11 NRBCs (range 1-40). By automated microscopy, 52% were positive, with on average 17 NRBCs (range 1-111). There was a good correlation between both manual and automated screening, but the NRBC yield from automated image analysis was found to be superior to that from manual screening (P=.0443), particularly when the NRBC count was >15. Seven (64%) of 11 XY fetuses were correctly diagnosed by FISH analysis of automatically detected cells, and all discrepancies were restricted to the lower cell-count range. We believe that automated microscopy and image analysis reduce the screening workload, are more sensitive than manual evaluation, and can be used to detect rare HbF-containing NRBCs in maternal blood. PMID:9837832

Farming in a fish tank.

PubMed

Youth, H

1992-01-01

Water, fish, and vegetables are all things that most developing countries do not have enough of. There is a method of food production called aquaculture that integrates fish and vegetable growing and conserves and purifies water at the same time. A working system that grows vegetables and fish for regional supermarkets in Massachusetts is a gravity fed system. At the top of the system is a 3,000 gallon fish rearing tank that measures 12 feet in diameter. Water trickles out of the tank and fish wastes are captured which can be composted and used in farm fields. The water goes into a bio filter that contains bacteria which convert harmful ammonia generated from fish waste into beneficial nitrate. Then the water flows into 100 foot long hydroponic tanks where lettuce grows. A 1/6 horsepower pump return the purified water to the fish tank and completes the cycle. The key to success is maintaining a balance between the fish nutrients and waste and the plants nutrients and waste. The system is estimated to produce 35,000 heads of lettuce and 2 tons of fish annually which translates into $23,500. The system could be adapted to developing countries with several modifications to reduce the start up cost.

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.

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.

Bypass system modification at Bonneville Dam on the Columbia River improved the survival of juvenile salmon

USGS Publications Warehouse

Ferguson, J.W.; Sandford, B.P.; Reagan, R.E.; Gilbreath, L.G.; Meyer, E.B.; Ledgerwood, R.D.; Adams, N.S.

2007-01-01

From 1987 to 1992, we evaluated a fish bypass system at Bonneville Dam Powerhouse 2 on the Columbia River. The survival of subyearling Chinook salmon Oncorhynchus tshawytscha released into the system ranged from 0.774 to 0.911 and was significantly lower than the survival of test fish released into turbines and the area immediately below the powerhouse where bypass system flow reentered the river. Yearling and subyearling Chinook salmon and yearling coho salmon O. kisutch released into the bypass system were injured or descaled. Also, levels of blood plasma cortisol and lactate were significantly higher in yearling and subyearling Chinook salmon that passed through the bypass system than in fish released directly into a net located over the bypass exit. This original system was then extensively modified using updated design criteria, and the site where juvenile fish reentered the river was relocated 2.8 km further downstream to reduce predation on bypassed fish by northern pikeminnow Ptychocheilus oregonensis. Based on studies conducted from 1999 to 2001, the new bypass system resulted in high fish survival, virtually no injuries to fish, fish passage times that were generally similar to water travel times, and mild stress responses from which fish recovered quickly. The mean estimated survival of subyearling Chinook salmon passing through the new bypass system was 0.946 in 2001, which was an usually low-flow year. Survival, physical condition, passage timing, and blood physiological indicators of stress were all useful metrics for assessing the performance of both bypass systems and are discussed. The engineering and hydraulic criteria used to design the new bypass system that resulted in improved fish passage conditions are described.

Influence of Melatonin on the Immune System of Fish: A Review

PubMed Central

Esteban, M. Ángeles; Cuesta, Alberto; Chaves-Pozo, Elena; Meseguer, José

2013-01-01

Endocrine-immune system interactions have been widely demonstrated in mammals, whereas in fish, these relationships remain unclear. Of the organs that constitute the endocrine system, the pineal gland and its secretory product melatonin act in the synchronization of daily and seasonal rhythms in most vertebrates, including fish. Seasonal differences in immunocompetence and disease prevalence have been well documented in humans. Seasonality also strongly influences the life history of fish by controlling the timing of physiological events, such as reproduction, food intake, locomotor activity, and growth performance. Apart from its synchronizing capabilities, the role of melatonin in physiological processes in fish is not thoroughly understood. The purpose of this review is to summarize current studies on the effects of melatonin on the fish immune system. These studies suggest that melatonin represents an important component of fish endocrine-immune system interactions. The elucidation of the defense mechanisms of fish will facilitate the development of health management tools to support the growing finfish aquaculture industry as well as address questions concerning the origins and evolution of the immune system in vertebrates. PMID:23579958

Influence of melatonin on the immune system of fish: a review.

PubMed

Esteban, M Ángeles; Cuesta, Alberto; Chaves-Pozo, Elena; Meseguer, José

2013-04-11

Endocrine-immune system interactions have been widely demonstrated in mammals, whereas in fish, these relationships remain unclear. Of the organs that constitute the endocrine system, the pineal gland and its secretory product melatonin act in the synchronization of daily and seasonal rhythms in most vertebrates, including fish. Seasonal differences in immunocompetence and disease prevalence have been well documented in humans. Seasonality also strongly influences the life history of fish by controlling the timing of physiological events, such as reproduction, food intake, locomotor activity, and growth performance. Apart from its synchronizing capabilities, the role of melatonin in physiological processes in fish is not thoroughly understood. The purpose of this review is to summarize current studies on the effects of melatonin on the fish immune system. These studies suggest that melatonin represents an important component of fish endocrine-immune system interactions. The elucidation of the defense mechanisms of fish will facilitate the development of health management tools to support the growing finfish aquaculture industry as well as address questions concerning the origins and evolution of the immune system in vertebrates.

Immediate systemic allergic reaction in an infant to fish allergen ingested through breast milk

PubMed Central

Arima, Takayasu; Campos-Alberto, Eduardo; Funakoshi, Hiraku; Inoue, Yuzaburo; Tomiita, Minako; Kohno, Yoichi

2016-01-01

This is a rare case report of systemic allergic reaction to fish allergen ingested through breast milk. Mother ate raw fish more than 3 times a week. Her consumption of fish was associated with urticaria and wheeze in an infant via breast-feeding. Fish-specific IgE antibodies were detected by skin prick test but not by in vitro IgE test. This case demonstrates that fish protein ingested by mother can cause an immediate systemic allergic reaction in offspring through breast-feeding. Although fish intake is generally recommended for prevention of allergy, one should be aware that frequent intake of fish by a lactating mother may sensitize the baby and induce an allergic reaction through breast-feeding. PMID:27803887

Long-term effect of rice-based farming systems on soil health.

PubMed

Bihari, Priyanka; Nayak, A K; Gautam, Priyanka; Lal, B; Shahid, M; Raja, R; Tripathi, R; Bhattacharyya, P; Panda, B B; Mohanty, S; Rao, K S

2015-05-01

Integrated rice-fish culture, an age-old farming system, is a technology which could produce rice and fish sustainably at a time by optimizing scarce resource use through complementary use of land and water. An understanding of microbial processes is important for the management of farming systems as soil microbes are the living part of soil organic matter and play critical roles in soil C and N cycling and ecosystem functioning of farming system. Rice-based integrated farming system model for small and marginal farmers was established in 2001 at Central Rice Research Institute, Cuttack, Odisha. The different enterprises of farming system were rice-fish, fish-fingerlings, fruits, vegetables, rice-fish refuge, and agroforestry. This study was conducted with the objective to assess the soil physicochemical properties, microbial population, carbon and nitrogen fractions, soil enzymatic activity, and productivity of different enterprises. The effect of enterprises induced significant changes in the chemical composition and organic matter which in turn influenced the activities of enzymes (urease, acid, and alkaline phosphatase) involved in the C, N, and P cycles. The different enterprises of long-term rice-based farming system caused significant variations in nutrient content of soil, which was higher in rice-fish refuge followed by rice-fish enterprise. Highest microbial populations and enzymatic properties were recorded in rice-fish refuge system because of waterlogging and reduced condition prolonged in this system leading to less decomposition of organic matter. The maximum alkaline phosphatase, urease, and FDA were observed in rice-fish enterprise. However, highest acid phosphatase and dehydrogenase activity were obtained in vegetable enterprise and fish-fingerlings enterprise, respectively.

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.

Emergy evaluation and economic analysis of three wetland fish farming systems in Nansi Lake area, China.

PubMed

Zhang, L X; Ulgiati, S; Yang, Z F; Chen, B

2011-03-01

Emergy and economic methods were used to evaluate and compare three fish production models, i.e., cage fish farming system, pond intensive fish rearing system and semi-natural extensive pond fish rearing system, in Nansi Lake area in China in the year 2007. The goal of this study was to understand the benefits and driving forces of selected fish production models from ecological and economic points of view. The study considered input structure, production efficiency, environmental impacts, economic viability and sustainability. Results show that the main difference among the three production systems was the emergy cost for fish feed associated with their feeding system, i.e., feeding on natural biomass such as plankton and grass or on commercial feedstock. As indicated by EYR, ELR and ESI, it can be clearly shown that the intensive production model with commercial feed is not a sustainable pattern. However, the point is that more environmentally sound patterns do not seem able to provide a competitive net profit in the short run. The intensive pond fish farming system had a net profit of 2.57E+03 $/ha, much higher than 1.27E+03 $/ha for cage fish farming system and slightly higher than 2.37E+03 $/ha for semi-natural fish farming system. With regard to the drivers of local farmer's decisions, the accessibility of land for the required use and investment ability determine the farmer's choice of the production model and the scale of operation, while other factors seem to have little effect. Theoretically, the development of environmentally sustainable production patterns, namely water and land conservation measures, greener feed as well as low waste systems is urgently needed, to keep production activities within the carrying capacity of ecosystems. Coupled emergy and economic analyses can provide better insight into the environmental and economic benefits of fish production systems and help solve the problems encountered during policy making. Copyright © 2010 Elsevier Ltd. All rights reserved.

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.

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

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.

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.

Detection of small surface vessels in near, medium, and far infrared spectral bands

NASA Astrophysics Data System (ADS)

Dulski, R.; Milewski, S.; Kastek, M.; Trzaskawka, P.; Szustakowski, M.; Ciurapinski, W.; Zyczkowski, M.

2011-11-01

Protection of naval bases and harbors requires close co-operation between security and access control systems covering land areas and those monitoring sea approach routes. The typical location of naval bases and harbors - usually next to a large city - makes it difficult to detect and identify a threat in the dense regular traffic of various sea vessels (i.e. merchant ships, fishing boats, tourist ships). Due to the properties of vessel control systems, such as AIS (Automatic Identification System), and the effectiveness of radar and optoelectronic systems against different targets it seems that fast motor boats called RIB (Rigid Inflatable Boat) could be the most serious threat to ships and harbor infrastructure. In the paper the process and conditions for the detection and identification of high-speed boats in the areas of ports and naval bases in the near, medium and far infrared is presented. Based on the results of measurements and recorded thermal images the actual temperature contrast delta T (RIB / sea) will be determined, which will further allow to specify the theoretical ranges of detection and identification of the RIB-type targets for an operating security system. The data will also help to determine the possible advantages of image fusion where the component images are taken in different spectral ranges. This will increase the probability of identifying the object by the multi-sensor security system equipped additionally with the appropriate algorithms for detecting, tracking and performing the fusion of images from the visible and infrared cameras.

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...

Polarized radiance distribution measurements of skylight. I. System description and characterization.

PubMed

Voss, K J; Liu, Y

1997-08-20

A new system to measure the natural skylight polarized radiance distribution has been developed. The system is based on a fish-eye lens, CCD camera system, and filter changer. With this system sequences of images can be combined to determine the linear polarization components of the incident light field. Calibration steps to determine the system 's polarization characteristics are described. Comparisons of the radiance measurements of this system and a simple pointing radiometer were made in the field and agreed within 10 % for measurements at 560 and 670 nm and 25 % at 860 nm. Polarization tests were done in the laboratory. The accuracy of the intensity measurements is estimated to be 10 %, while the accuracy of measurements of elements of the Mueller matrix are estimated to be 2 %.

Breaking Snake Camouflage: Humans Detect Snakes More Accurately than Other Animals under Less Discernible Visual Conditions.

PubMed

Kawai, Nobuyuki; He, Hongshen

2016-01-01

Humans and non-human primates are extremely sensitive to snakes as exemplified by their ability to detect pictures of snakes more quickly than those of other animals. These findings are consistent with the Snake Detection Theory, which hypothesizes that as predators, snakes were a major source of evolutionary selection that favored expansion of the visual system of primates for rapid snake detection. Many snakes use camouflage to conceal themselves from both prey and their own predators, making it very challenging to detect them. If snakes have acted as a selective pressure on primate visual systems, they should be more easily detected than other animals under difficult visual conditions. Here we tested whether humans discerned images of snakes more accurately than those of non-threatening animals (e.g., birds, cats, or fish) under conditions of less perceptual information by presenting a series of degraded images with the Random Image Structure Evolution technique (interpolation of random noise). We find that participants recognize mosaic images of snakes, which were regarded as functionally equivalent to camouflage, more accurately than those of other animals under dissolved conditions. The present study supports the Snake Detection Theory by showing that humans have a visual system that accurately recognizes snakes under less discernible visual conditions.

Breaking Snake Camouflage: Humans Detect Snakes More Accurately than Other Animals under Less Discernible Visual Conditions

PubMed Central

He, Hongshen

2016-01-01

Humans and non-human primates are extremely sensitive to snakes as exemplified by their ability to detect pictures of snakes more quickly than those of other animals. These findings are consistent with the Snake Detection Theory, which hypothesizes that as predators, snakes were a major source of evolutionary selection that favored expansion of the visual system of primates for rapid snake detection. Many snakes use camouflage to conceal themselves from both prey and their own predators, making it very challenging to detect them. If snakes have acted as a selective pressure on primate visual systems, they should be more easily detected than other animals under difficult visual conditions. Here we tested whether humans discerned images of snakes more accurately than those of non-threatening animals (e.g., birds, cats, or fish) under conditions of less perceptual information by presenting a series of degraded images with the Random Image Structure Evolution technique (interpolation of random noise). We find that participants recognize mosaic images of snakes, which were regarded as functionally equivalent to camouflage, more accurately than those of other animals under dissolved conditions. The present study supports the Snake Detection Theory by showing that humans have a visual system that accurately recognizes snakes under less discernible visual conditions. PMID:27783686

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.

Remote high-definition rotating video enables fast spatial survey of marine underwater macrofauna and habitats.

PubMed

Pelletier, Dominique; Leleu, Kévin; Mallet, Delphine; Mou-Tham, Gérard; Hervé, Gilles; Boureau, Matthieu; Guilpart, Nicolas

2012-01-01

Observing spatial and temporal variations of marine biodiversity from non-destructive techniques is central for understanding ecosystem resilience, and for monitoring and assessing conservation strategies, e.g. Marine Protected Areas. Observations are generally obtained through Underwater Visual Censuses (UVC) conducted by divers. The problems inherent to the presence of divers have been discussed in several papers. Video techniques are increasingly used for observing underwater macrofauna and habitat. Most video techniques that do not need the presence of a diver use baited remote systems. In this paper, we present an original video technique which relies on a remote unbaited rotating remote system including a high definition camera. The system is set on the sea floor to record images. These are then analysed at the office to quantify biotic and abiotic sea bottom cover, and to identify and count fish species and other species like marine turtles. The technique was extensively tested in a highly diversified coral reef ecosystem in the South Lagoon of New Caledonia, based on a protocol covering both protected and unprotected areas in major lagoon habitats. The technique enabled to detect and identify a large number of species, and in particular fished species, which were not disturbed by the system. Habitat could easily be investigated through the images. A large number of observations could be carried out per day at sea. This study showed the strong potential of this non obtrusive technique for observing both macrofauna and habitat. It offers a unique spatial coverage and can be implemented at sea at a reasonable cost by non-expert staff. As such, this technique is particularly interesting for investigating and monitoring coastal biodiversity in the light of current conservation challenges and increasing monitoring needs.

The role of fish in a globally changing food system

USGS Publications Warehouse

Lynch, Abigail J.; MacMillan, J. Randy

2017-01-01

Though humans have been fishing for food since they first created tools to hunt, modern food systems are predominately terrestrial focused and fish are frequently overlooked. Yet, within the global food system, fish play an important role in meeting current and future food needs. Capture fisheries are the last large-scale “wild” food, and aquaculture is the fastest growing food production sector in the world. Currently, capture fisheries and aquaculture provide 4.3 billion people with at least 15% of their animal protein. In addition to providing protein and calories, fish are important sources of critical vitamins and vital nutrients that are difficult to acquire through other food sources. As the climate changes, human populations will continue to grow, cultural tastes will evolve, and fish populations will respond. Sustainable fisheries and aquaculture are poised to fill demand for food not met by terrestrial food systems. Climate change and other global changes will increase, decrease, or modify many wild fish populations and aquaculture systems. Understanding the knowledge gaps around these implications for global change on fish production is critical. Applied research and adaptive management techniques can assist with the necessary evolution of sustainable food systems to include a stronger emphasis on fish and other aquatic organisms.

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.

The influence of external subsidies on diet, growth and Hg concentrations of freshwater sport fish: implications for management and fish consumption advisories

USGS Publications Warehouse

Lepak, J.M.; Hooten, M.B.; Johnson, B.M.

2012-01-01

Mercury (Hg) contamination in sport fish is a global problem. In freshwater systems, food web structure, sport fish sex, size, diet and growth rates influence Hg bioaccumulation. Fish stocking is a common management practice worldwide that can introduce external energy and contaminants into freshwater systems. Thus, stocking can alter many of the factors that influence Hg concentrations in sport fish. Here we evaluated the influence of external subsidies, in the form of hatchery-raised rainbow trout Oncorhynchus mykiss on walleye Sander vitreus diet, growth and Hg concentrations in two freshwater systems. Stocking differentially influenced male and female walleye diets and growth, producing a counterintuitive size-contamination relationship. Modeling indicated that walleye growth rate and diet were important explanatory variables when predicting Hg concentrations. Thus, hatchery contributions to freshwater systems in the form of energy and contaminants can influence diet, growth and Hg concentrations in sport fish. Given the extensive scale of fish stocking, and the known health risks associated with Hg contamination, this represents a significant issue for managers monitoring and manipulating freshwater food web structures, and policy makers attempting to develop fish consumption advisories to protect human health in stocked systems.

The influence of external subsidies on diet, growth and Hg concentrations of freshwater sport fish: implications for management and fish consumption advisories.

PubMed

Lepak, Jesse M; Hooten, Mevin B; Johnson, Brett M

2012-10-01

Mercury (Hg) contamination in sport fish is a global problem. In freshwater systems, food web structure, sport fish sex, size, diet and growth rates influence Hg bioaccumulation. Fish stocking is a common management practice worldwide that can introduce external energy and contaminants into freshwater systems. Thus, stocking can alter many of the factors that influence Hg concentrations in sport fish. Here we evaluated the influence of external subsidies, in the form of hatchery-raised rainbow trout Oncorhynchus mykiss on walleye Sander vitreus diet, growth and Hg concentrations in two freshwater systems. Stocking differentially influenced male and female walleye diets and growth, producing a counterintuitive size-contamination relationship. Modeling indicated that walleye growth rate and diet were important explanatory variables when predicting Hg concentrations. Thus, hatchery contributions to freshwater systems in the form of energy and contaminants can influence diet, growth and Hg concentrations in sport fish. Given the extensive scale of fish stocking, and the known health risks associated with Hg contamination, this represents a significant issue for managers monitoring and manipulating freshwater food web structures, and policy makers attempting to develop fish consumption advisories to protect human health in stocked systems.

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.

Panoramic stereo sphere vision

NASA Astrophysics Data System (ADS)

Feng, Weijia; Zhang, Baofeng; Röning, Juha; Zong, Xiaoning; Yi, Tian

2013-01-01

Conventional stereo vision systems have a small field of view (FOV) which limits their usefulness for certain applications. While panorama vision is able to "see" in all directions of the observation space, scene depth information is missed because of the mapping from 3D reference coordinates to 2D panoramic image. In this paper, we present an innovative vision system which builds by a special combined fish-eye lenses module, and is capable of producing 3D coordinate information from the whole global observation space and acquiring no blind area 360°×360° panoramic image simultaneously just using single vision equipment with one time static shooting. It is called Panoramic Stereo Sphere Vision (PSSV). We proposed the geometric model, mathematic model and parameters calibration method in this paper. Specifically, video surveillance, robotic autonomous navigation, virtual reality, driving assistance, multiple maneuvering target tracking, automatic mapping of environments and attitude estimation are some of the applications which will benefit from PSSV.

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

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.

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

[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.

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.

Social interactions among grazing reef fish drive material flux in a coral reef ecosystem.

PubMed

Gil, Michael A; Hein, Andrew M

2017-05-02

In human financial and social systems, exchanges of information among individuals cause speculative bubbles, behavioral cascades, and other correlated actions that profoundly influence system-level function. Exchanges of information are also widespread in ecological systems, but their effects on ecosystem-level processes are largely unknown. Herbivory is a critical ecological process in coral reefs, where diverse assemblages of fish maintain reef health by controlling the abundance of algae. Here, we show that social interactions have a major effect on fish grazing rates in a reef ecosystem. We combined a system for observing and manipulating large foraging areas in a coral reef with a class of dynamical decision-making models to reveal that reef fish use information about the density and actions of nearby fish to decide when to feed on algae and when to flee foraging areas. This "behavioral coupling" causes bursts of feeding activity that account for up to 68% of the fish community's consumption of algae. Moreover, correlations in fish behavior induce a feedback, whereby each fish spends less time feeding when fewer fish are present, suggesting that reducing fish stocks may not only reduce total algal consumption but could decrease the amount of algae each remaining fish consumes. Our results demonstrate that social interactions among consumers can have a dominant effect on the flux of energy and materials through ecosystems, and our methodology paves the way for rigorous in situ measurements of the behavioral rules that underlie ecological rates in other natural systems.

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.

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.

New optical package and algorithms for accurate estimation and interactive recording of the cloud cover information over land and sea

NASA Astrophysics Data System (ADS)

Krinitskiy, Mikhail; Sinitsyn, Alexey; Gulev, Sergey

2014-05-01

Cloud fraction is a critical parameter for the accurate estimation of short-wave and long-wave radiation - one of the most important surface fluxes over sea and land. Massive estimates of the total cloud cover as well as cloud amount for different layers of clouds are available from visual observations, satellite measurements and reanalyses. However, these data are subject of different uncertainties and need continuous validation against highly accurate in-situ measurements. Sky imaging with high resolution fish eye camera provides an excellent opportunity for collecting cloud cover data supplemented with additional characteristics hardly available from routine visual observations (e.g. structure of cloud cover under broken cloud conditions, parameters of distribution of cloud dimensions). We present operational automatic observational package which is based on fish eye camera taking sky images with high resolution (up to 1Hz) in time and a spatial resolution of 968x648px. This spatial resolution has been justified as an optimal by several sensitivity experiments. For the use of the package at research vessel when the horizontal positioning becomes critical, a special extension of the hardware and software to the package has been developed. These modules provide the explicit detection of the optimal moment for shooting. For the post processing of sky images we developed a software realizing the algorithm of the filtering of sunburn effect in case of small and moderate could cover and broken cloud conditions. The same algorithm accurately quantifies the cloud fraction by analyzing color mixture for each point and introducing the so-called "grayness rate index" for every pixel. The accuracy of the algorithm has been tested using the data collected during several campaigns in 2005-2011 in the North Atlantic Ocean. The collection of images included more than 3000 images for different cloud conditions supplied with observations of standard parameters. The system is fully autonomous and has a block for digital data collection at the hard disk. The system has been tested for a wide range of open ocean cloud conditions and we will demonstrate some pilot results of data processing and physical interpretation of fractional cloud cover estimation.

Danio rerio: Small Fish Making a Big Splash in Leukemia.

PubMed

Squiban, Barbara; Frazer, J Kimble

2014-06-01

Zebrafish ( Danio rerio ) are widely used for developmental biology studies. In the past decade, D. rerio have become an important oncology model as well. Leukemia is one type of cancer where zebrafish are particularly valuable. As vertebrates, fish have great anatomic and biologic similarity to humans, including their hematopoietic and immune systems. As an experimental platform, D. rerio offer many advantages that mammalian models lack. These include their ease of genetic manipulation, capacity for imaging, and suitability for large-scale phenotypic and drug screens. In this review, we present examples of these strategies and others to illustrate how zebrafish have been and can be used to study leukemia. Besides appraising the techniques researchers apply and introducing the leukemia models they have created, we also highlight recent and exciting discoveries made using D. rerio with an eye to where the field is likely headed.

NASA's Ship-Aircraft Bio-Optical Research (SABOR)

NASA Image and Video Library

2014-08-25

Fixing the "Fish" On July 19, 2014, Wayne Slade of Sequoia Scientific, and Allen Milligan of Oregon State University, made adjustments to the "fish" that researchers used to hold seawater collected from a depth of about 3 meters (10 feet) while the ship was underway. NASA's Ship-Aircraft Bio-Optical Research (SABOR) experiment is a coordinated ship and aircraft observation campaign off the Atlantic coast of the United States, an effort to advance space-based capabilities for monitoring microscopic plants that form the base of the marine food chain. Read more: 1.usa.gov/WWRVzj Credit: NASA/SABOR/Wayne Slade, Sequoia Scientific .NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

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

Comparison of Selected Metals Content in Cambodian Striped Snakehead Fish (Channa striata) Using Solar Drying System and Open Sun Drying

PubMed Central

Abu Bakar, Nur Faizah; Fudholi, Ahmad; Ruslan, Mohd Hafidz; Saroeun, Im

2015-01-01

The content of 12 elements in Cambodian dried striped snakehead fish was determined using inductively coupled plasma mass spectrometry. The present study compares the level of the trace toxic metals and nutritional trace elements in the fish processed using solar drying system (SDS) and open sun drying (OSD). The skin of SDS fish has lower level of As, Pb, and Cd compared to the OSD sample. As such, the flesh of the fish accumulated higher amount of toxic metals during OSD compared to SDS. However, arsenic was detected in both samples within the safe limit. The nutritional elements (Fe, Mn, Mg, Se, Mo, Cu, Ni, and Cr) were higher in the skin sample SDS fish compared to OSD fish. These beneficial metals were not accumulated in the flesh sample SDS fish demonstrating lower level compared to drying under conventional system. The reddish coloration of the SDS fish was due to the presence of high Cu content in both the skin and flesh samples which possibly account for no mold formation 5 days after packaging. As conclusion, drying of Cambodian C. striata using solar-assisted system has proven higher content of the nutritious elements compared to using the conventional system despite only slight difference in the toxic metals level between the two systems. PMID:25688274

The Teleost Octavolateralis System: Structure and Function

NASA Technical Reports Server (NTRS)

Popper, Arthur N.

1996-01-01

This paper considers the detection of vibrational signals (including sound) by the two components of the octavolateralis system, the ear and mechanosensory lateral line. Together, these systems provide fishes with a good deal of information about their surrounding environment, and enable fishes to detect both predators and prey. While the mechanisms by which fishes and zooplankton produce and detect signals may differ, it is clear that the physical principles underlying the signals themselves are identical, no matter whether we are dealing with fish or zooplankton. Thus, an understanding of signal production and detection mechanisms by fishes can be of significant help in understanding how similar systems would function in zooplankton.

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.

The oxidation of drugs by fishes

USGS Publications Warehouse

Buhler, Donald R.; Rasmusson, Mary E.

1968-01-01

1. Fish liver microsomal systems have been found to catalyze the hydroxylation of aniline and acetanilide, the N-demethylation of aminopyrine and the O-dealkylation of phenacetin.2. These systems are similar to the corresponding mammalian enzymes and they may be considered to be mixed function oxidase since they require NADPH and oxygen. An absolute requirement for oxygen, however, was difficult to demonstrate for the hepatic phenacetin cleavage system from fish.3. Microsomal drug metabolizing systems from fish have temperature optima which are considerably lower than those of corresponding mammalian systems

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.

Cold water corals - Converting short term scientific excitement into long term public interest

NASA Astrophysics Data System (ADS)

Maestad, K.

2009-04-01

The Vesteraalen area off the Northern Norwegian coast is of ecological importance as a spawning ground for several fish stocks and as a corridor for migrating mature fish and drifting fish larvae for other stocks. The area is also of great interest to oil exploration companies for its hitherto untapped energy supplies. In the midst of it all, there are a number of cold-water coral reefs. Researchers at the Institute of Marine Research in Norway have constructed a sophisticated system for monitoring habitats around the cold-water corals and their environment over time. Two so-called landers will be placed next to coral reefs, will be equipped with echo sounders, camera, hydrophone, acoustic current profiler, CTD-sensor and sediment traps in March 09. This will provide high quality data regarding both physical conditions and biological activity. The sensors will make it possible to observe how different species interact with each other, with particular focus on the activity of fish and how they use the reef habitat. The system will have the capacity to transmit data live from the ocean floor. Creating attention in national media regarding such a ground-breaking project is not all that difficult. Already, the Norwegian national TV channel NRK has confirmed participation on the cruise that will deploy the landers. However, this project also presents communication challenges. One of which is to find a way of making echogram images of the reef understandable ("readable") to people not familiar with interpreting echo sounder signals. This will be especially important if it is decided to make the data from the coral reef available live on the internet. Furthermore, the aim will be to create interest amongst specific audiences in following the life in and around the coral reef over time.

Key Contributors to Variations in Fish Mercury Within and Among Freshwater Reservoirs in Oklahoma, USA

PubMed Central

Dong, Zhao; Lynch, Robert A.; Schaider, Laurel A.

2017-01-01

Elevated fish mercury (Hg) concentrations in freshwater ecosystems worldwide are a significant human and ecological health concern. Mercury bioaccumulation and biomagnification in lakes and reservoirs are controlled by numerous biogeochemical and ecological factors, contributing to variability in fish Hg concentrations both within and among systems. We measured total mercury concentrations ([THg]) and stable isotopes (δ15N, δ13C) in over 30 fish species in two connected subtropical freshwater reservoirs (Grand Lake and Lake Hudson, Oklahoma, USA), their tributaries, and local farm ponds, all of which are potentially impacted by nearby atmospheric Hg sources. We also conducted an inter-system analysis among 61 reservoirs in Oklahoma to explore biological, chemical and physical factors associated with fish [THg] across systems. We found that [THg] for most species in Grand Lake and Lake Hudson were relatively low compared to other reservoirs in Oklahoma. There were significant spatial variations in many species within and between Grand Lake and Lake Hudson, even after accounting for length and/or trophic position (based on δ15N). Fish in local farm ponds, commonly used in the agricultural regions for raising game fish, had 2–17 times higher [THg] than fish of similar length in nearby reservoirs. The inter-system analysis revealed that pH, water color, rainfall, and nutrients are the best predictors of fish [THg] across systems. Our results provide insight into the key factors associated with fish [THg] variations both within and across systems, and may be useful for exposure assessment and for identifying sites and water bodies prone to high fish [THg] as monitoring priorities. PMID:26729635

Implantable acoustic-beacon automatic fish-tracking system

NASA Technical Reports Server (NTRS)

Mayhue, R. J.; Lovelady, R. W.; Ferguson, R. L.; Richards, C. E.

1977-01-01

A portable automatic fish tracking system was developed for monitoring the two dimensional movements of small fish within fixed areas of estuarine waters and lakes. By using the miniature pinger previously developed for this application, prototype tests of the system were conducted in the York River near the Virginia Institute of Marine Science with two underwater listening stations. Results from these tests showed that the tracking system could position the miniature pinger signals to within + or - 2.5 deg and + or - 135 m at ranges up to 2.5 km. The pingers were implanted in small fish and were successfully tracked at comparable ranges. No changes in either fish behavior or pinger performance were observed as a result of the implantation. Based on results from these prototype tests, it is concluded that the now commercially available system provides an effective approach to underwater tracking of small fish within a fixed area of interest.

Use of a parallel artificial membrane system to evaluate passive absorption and elimination in small fish.

PubMed

Kwon, Jung-Hwan; Katz, Lynn E; Liljestrand, Howard M

2006-12-01

A parallel artificial lipid membrane system was developed to mimic passive mass transfer of hydrophobic organic chemicals in fish. In this physical model system, a membrane filter-supported lipid bilayer separates two aqueous phases that represent the external and internal aqueous environments of fish. To predict bioconcentration kinetics in small fish with this system, literature absorption and elimination rates were analyzed with an allometric diffusion model to quantify the mass transfer resistances in the aqueous and lipid phases of fish. The effect of the aqueous phase mass transfer resistance was controlled by adjusting stirring intensity to mimic bioconcentration rates in small fish. Twenty-three simple aromatic hydrocarbons were chosen as model compounds for purposes of evaluation. For most of the selected chemicals, literature absorption/elimination rates fall into the range predicted from measured membrane permeabilities and elimination rates of the selected chemicals determined by the diffusion model system.

Fish pass assessment by remote control: a novel framework for quantifying the hydraulics at fish pass entrances

NASA Astrophysics Data System (ADS)

Kriechbaumer, Thomas; Blackburn, Kim; Gill, Andrew; Breckon, Toby; Everard, Nick; Wright, Ros; Rivas Casado, Monica

2014-05-01

Fragmentation of aquatic habitats can lead to the extinction of migratory fish species with severe negative consequences at the ecosystem level and thus opposes the target of good ecological status of rivers defined in the EU Water Framework Directive (WFD). In the UK, the implementation of the EU WFD requires investments in fish pass facilities of estimated 532 million GBP (i.e. 639 million Euros) until 2027 to ensure fish passage at around 3,000 barriers considered critical. Hundreds of passes have been installed in the past. However, monitoring studies of fish passes around the world indicate that on average less than half of the fish attempting to pass such facilities are actually successful. There is a need for frameworks that allow the rapid identification of facilities that are biologically effective and those that require enhancement. Although there are many environmental characteristics that can affect fish passage success, past research suggests that variations in hydrodynamic conditions, reflected in water velocities, velocity gradients and turbulences, are the major cues that fish use to seek migration pathways in rivers. This paper presents the first steps taken in the development of a framework for the rapid field-based quantification of the hydraulic conditions downstream of fish passes and the assessment of the attractivity of fish passes for salmonids and coarse fish in UK rivers. For this purpose, a small-sized remote control platform carrying an acoustic Doppler current profiler (ADCP), a GPS unit, a stereo camera and an inertial measurement unit has been developed. The large amount of data on water velocities and depths measured by the ADCP within relatively short time is used to quantify the spatial and temporal distribution of water velocities. By matching these hydraulic features with known preferences of migratory fish, it is attempted to identify likely migration routes and aggregation areas at barriers as well as hydraulic features that may distract fish away from fish pass entrances. The initial steps of the framework development have focused on the challenge of precise spatial data referencing in areas with limited sky view to navigation satellites. Platform tracking with a motorised Total Station, various satellite-based positioning solutions and simultaneous localisation and mapping (SLAM) based on stereo images have been tested. The effect of errors in spatial data referencing on ADCP-derived maps of flow features and bathymetry will be quantified through simultaneous deployment of these navigation technologies and the ADCP. This will inform the selection of a cost-effective platform positioning system in practice. Further steps will cover the quantification of uncertainties in ADCP data caused by highly turbulent flows and the identification of suitable ADCP data sampling strategies at fish passes. The final framework for fish pass assessment can contribute to an improved understanding of the interaction of fish and the complex hydraulic river environment.

Disposition of xenobiotic chemicals and metabolites in marine organisms.

PubMed Central

Varanasi, U; Stein, J E

1991-01-01

Studies with several bottom fish species from urban waterways show that of the identified xenobiotic chemicals in bottom sediments, polycylic aromatic hydrocarbons (PAHs) are the most strongly associated with the prevalence of liver lesions, including neoplasms. Accordingly, there is concern about the transfer of contaminants, such as PAHs, from aquatic species to humans. Because PAHs exert their toxicity only after being biotransformed, increasing attention has been focused on the ability of aquatic organisms to metabolize these chemicals. Overall, the results of both laboratory and field studies show that generally low levels (nanograms per gram wet weight) of a few low molecular weight PAHs may be present in edible tissue of fish from contaminated areas and that high molecular weight PAHs, such as the carcinogen benzo(a)pyrene, will rarely be detected because of extensive metabolism. Additionally, the results from a few studies suggest that even though interactions between xenobiotics can affect both biochemical and physiological systems to alter the disposition of PAHs in fish, these interactions do not markedly change the relative proportions of metabolites to parent PAH in tissues. Thus, these studies clearly demonstrate that to obtain some insight into the questions of whether there is any risk to human health from consuming fish and crustaceans from urban areas, techniques must be developed that measure metabolites of carcinogens, such as PAHs, in edible tissue. Initial attempts may focus on semiquantitative methods that permit rapid assessment of the level of metabolites in edible tissues of fish and crustaceans from many urban areas.(ABSTRACT TRUNCATED AT 250 WORDS) Images FIGURE 4. FIGURE 4. FIGURE 4. PMID:2050086

Implementing an open-access CASA software for the assessment of stallion sperm motility: Relationship with other sperm quality parameters.

PubMed

Giaretta, Elisa; Munerato, Mauro; Yeste, Marc; Galeati, Giovanna; Spinaci, Marcella; Tamanini, Carlo; Mari, Gaetano; Bucci, Diego

2017-01-01

Setting an open-access computer assisted sperm analysis (CASA) may benefit the evaluation of motility in mammalian sperm, especially when economic constraints do not allow the use of a commercial system. There have been successful attempts to develop such a device in Zebra fish sperm and the system has been used in very few studies on mammalian spermatozoa. Against this background, the present study aimed at developing an open-access CASA system for mammalian sperm using the horse as a model and based upon the Image J software previously established for Zebra fish sperm. Along with determining the sperm progressive motility and other kinetic parameters (such as amplitude of lateral head displacement), the "results" window was adjusted to simplify subsequent statistical analyses. The path window was enriched with colored sperm trajectories on the basis of the subpopulation they belong to and a number that allowed the sperm track to be associated to the sperm motility data shown in the "results" window. Data obtained from the novel plugin (named as CASA_bgm) were compared with those of the commercial CASA Hamilton-Thorn IVOS Vers.12, through Bland Altman's plots. While the percentage of total and progressive motile sperm, VCL, VAP, VSL, LIN and STR and ALH were in agreement with those obtained with the commercial system, BCF significantly differed between the two systems probably due to their settings. Interestingly, a positive and significant correlation between the percentages of total motile sperm evaluated through CASA_bgm and those showing high mitochondrial membrane potential evaluated by JC-1 staining was found. In conclusion, CASA_bgm ImageJ plugin could be useful and reliable for stallion sperm motility analysis and it is our aim to apply this system to other mammalian species. Copyright © 2016 Elsevier B.V. All rights reserved.

"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.

Chemical Ototoxicity of the Fish Inner Ear and Lateral Line.

PubMed

Coffin, Allison B; Ramcharitar, John

2016-01-01

Hair cell-driven mechanosensory systems are crucial for successful execution of a number of behaviors in fishes, and have emerged as good models for exploring questions relevant to human hearing. This review focuses on ototoxic effects in the inner ear and lateral line system of fishes. We specifically examine studies where chemical ototoxins such as aminoglycoside antibiotics have been employed as tools to disable the lateral line. Lateral line ablation results in alterations to feeding behavior and orientation to water current in a variety of species. However, neither behavior is abolished in the presence of additional sensory cues, supporting the hypothesis that many fish behaviors are driven by multisensory integration. Within biomedical research, the larval zebrafish lateral line has become an important model system for understanding signaling mechanisms that contribute to hair cell death and for developing novel pharmacological therapies that protect hair cells from ototoxic damage. Furthermore, given that fishes robustly regenerate damaged hair cells, ototoxin studies in fishes have broadened our understanding of the molecular and genetic events in an innately regenerative system, offering potential targets for mammalian hair cell regeneration. Collectively, studies of fish mechanosensory systems have yielded insight into fish behavior and in mechanisms of hair cell death, protection, and regeneration.

Fish community responses to green tides in shallow estuarine and coastal areas

NASA Astrophysics Data System (ADS)

Le Luherne, E.; Réveillac, E.; Ponsero, A.; Sturbois, A.; Ballu, S.; Perdriau, M.; Le Pape, O.

2016-06-01

All over the world, numerous bays and estuarine systems that are known to shelter essential fish habitats are experiencing proliferations of green macroalgae known as green tides. Although the processes that enhance green tides in response to nutrient enrichment are well known, their consequences for ecological communities -especially for ichthyofauna- remain poorly studied. To estimate these consequences, this analysis focused on the two types of shallow systems that are experiencing green tides: sandy beaches and estuarine mudflats. In these two systems, macroalgae proliferation and fish community were surveyed along seasonal cycles at control and impacted sites that shared similar physico-chemical parameters and sediment structure. To analyse the consequences of green tides on the fish community, a Before-After Control-Impact approach was used. This approach reveals no difference between fish communities at the control and impacted sites before the macroalgal bloom. Then, it underlines an influence of green tides on the fish community, and this influence varies according to the composition, density and duration of the macroalgal bloom. Indeed, when intertidal systems experienced short proliferation and/or weak density, green tides did not seem to impact the fish community. However, when green macroalgae proliferated in large quantities and/or when the proliferation lasted for long periods, the fish community was significantly affected. These modifications in the fish community led to a significant decrease in fish species diversity and density until fish disappeared from impacted sites at high proliferations. Furthermore, the response of fish species to green tides differed according to their functional guilds. Negative consequences for benthic and marine juvenile fish species were beginning at low proliferations, whereas for pelagic fish species they occurred only at high proliferations. Thus, green tides significantly affect fish habitat suitability because they lead to changes in the composition of the fish community and eventually to the local disappearance of fish at high proliferations.

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.

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.

Prevalence of Clonorchis sinensis Metacercariae in Fish from Water Systems of Seomjin-gang (River).

PubMed

Sohn, Woon-Mok; Na, Byoung-Kuk; Cho, Shin-Hyeong; Park, Mi-Yeoun; Kim, Cheon-Hyeon; Hwang, Min-Ah; No, Kyeong-Woo; Yoon, Ki-Bok; Lim, Hyun-Cheol

2017-06-01

The prevalence of Clonorchis sinensis metacercariae ( Cs Mc) was examined in freshwater fish from the water systems of Seomjin-gang (River), the Republic of Korea. Total 1,604 fish from 7 local sites of Seomjin-gang were examined by artificial digestion methods. The metacercariae of C. sinensis were detected in 102 (39.8%) out of 256 fish (14 species) from the upper reaches of Seomjin-gang, i.e., Osucheon (22.3% in 6 fish species) in Imsil-gun, and Seomjin-gang (63.9% in 9 fish species) in Sunchang-gun, Jeollabuk-do. Their average density was 9.0 per infected fish. They were also found in 132 (48.0%) out of 275 fish (12 spp.) from the middle reaches of Seomjin-gang, i.e., Songdaecheon (58.9% in 4 fish species) in Namwon-si, Jeollabuk-do, and Seomjin-gang (45.2% in 10 fish species) in Gokseong-gun, Jeollanam-do. Their average density was 21.0 per infected fish. Cs Mc were detected in 77 (56.6%) out of 136 fish (11 species) from the lower reaches of Seomjin-gang, i.e., Seomjin-gang (73.3% in 11 fish species) in Gurye-gun, Jeollanam-do, and Namsancheon (8.6% in 1 fish species) in Hadong-gun, Gyeongsangnam-do. Their average density was 64.9 per infected fish. The metacercariae of Metorchis orientalis were also detected in 6 fish species from 4 sites of Seomjin-gang. Conclusively, it has been confirmed that Cs Mc are more or less prevalent in fish from some water systems of Seomjin-gang in Korea.

Prevalence of Clonorchis sinensis Metacercariae in Fish from Water Systems of Seomjin-gang (River)

PubMed Central

Sohn, Woon-Mok; Na, Byoung-Kuk; Cho, Shin-Hyeong; Park, Mi-Yeoun; Kim, Cheon-Hyeon; Hwang, Min-Ah; No, Kyeong-Woo; Yoon, Ki-Bok; Lim, Hyun-Cheol

2017-01-01

The prevalence of Clonorchis sinensis metacercariae (CsMc) was examined in freshwater fish from the water systems of Seomjin-gang (River), the Republic of Korea. Total 1,604 fish from 7 local sites of Seomjin-gang were examined by artificial digestion methods. The metacercariae of C. sinensis were detected in 102 (39.8%) out of 256 fish (14 species) from the upper reaches of Seomjin-gang, i.e., Osucheon (22.3% in 6 fish species) in Imsil-gun, and Seomjin-gang (63.9% in 9 fish species) in Sunchang-gun, Jeollabuk-do. Their average density was 9.0 per infected fish. They were also found in 132 (48.0%) out of 275 fish (12 spp.) from the middle reaches of Seomjin-gang, i.e., Songdaecheon (58.9% in 4 fish species) in Namwon-si, Jeollabuk-do, and Seomjin-gang (45.2% in 10 fish species) in Gokseong-gun, Jeollanam-do. Their average density was 21.0 per infected fish. CsMc were detected in 77 (56.6%) out of 136 fish (11 species) from the lower reaches of Seomjin-gang, i.e., Seomjin-gang (73.3% in 11 fish species) in Gurye-gun, Jeollanam-do, and Namsancheon (8.6% in 1 fish species) in Hadong-gun, Gyeongsangnam-do. Their average density was 64.9 per infected fish. The metacercariae of Metorchis orientalis were also detected in 6 fish species from 4 sites of Seomjin-gang. Conclusively, it has been confirmed that CsMc are more or less prevalent in fish from some water systems of Seomjin-gang in Korea. PMID:28719955

Completing fishing monitoring with spaceborne Vessel Detection System (VDS) and Automatic Identification System (AIS) to assess illegal fishing in Indonesia.

PubMed

Longépé, Nicolas; Hajduch, Guillaume; Ardianto, Romy; Joux, Romain de; Nhunfat, Béatrice; Marzuki, Marza I; Fablet, Ronan; Hermawan, Indra; Germain, Olivier; Subki, Berny A; Farhan, Riza; Muttaqin, Ahmad Deni; Gaspar, Philippe

2017-10-26

The Indonesian fisheries management system is now equipped with the state-of-the-art technologies to deter and combat Illegal, Unreported and Unregulated (IUU) fishing. Since October 2014, non-cooperative fishing vessels can be detected from spaceborne Vessel Detection System (VDS) based on high resolution radar imagery, which directly benefits to coordinated patrol vessels in operation context. This study attempts to monitor the amount of illegal fishing in the Arafura Sea based on this new source of information. It is analyzed together with Vessel Monitoring System (VMS) and satellite-based Automatic Identification System (Sat-AIS) data, taking into account their own particularities. From October 2014 to March 2015, i.e. just after the establishment of a new moratorium by the Indonesian authorities, the estimated share of fishing vessels not carrying VMS, thus being illegal, ranges from 42 to 47%. One year later in January 2016, this proportion decreases and ranges from 32 to 42%. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

[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.

Effects of Sex Steroids on Fish Leukocytes

PubMed Central

Cabas, Isabel

2018-01-01

In vertebrates, in addition to their classically reproductive functions, steroids regulate the immune system. This action is possible mainly due to the presence of steroid receptors in the different immune cell types. Much evidence suggests that the immune system of fish is vulnerable to xenosteroids, which are ubiquitous in the aquatic environment. In vivo and in vitro assays have amply demonstrated that oestrogens interfere with both the innate and the adaptive immune system of fish by regulating the main leukocyte activities and transcriptional genes. They activate nuclear oestrogen receptors and/or G-protein coupled oestrogen receptor. Less understood is the role of androgens in the immune system, mainly due to the complexity of the transcriptional regulation of androgen receptors in fish. The aim of this manuscript is to review our present knowledge concerning the effect of sex steroid hormones and the presence of their receptors on fish leukocytes, taking into consideration that the studies performed vary as regard the fish species, doses, exposure protocols and hormones used. Moreover, we also include evidence of the probable role of progestins in the regulation of the immune system of fish. PMID:29315244

Development and use of in-stream PIT-tag detection systems to assess movement behavior of fish in tributaries of the Columbia River Basin, USA

USGS Publications Warehouse

Connolly, P.J.; Jezorek, I.G.; Prentice, E.F.

2005-01-01

We have developed detector systems for fish implanted with Passive Integrated Transponder (PIT) tags to assess their movement behavior and habitat use within fast flowing streams. Fish tested have primarily been wild anadromous and resident forms of rainbow trout Oncorhynchus mykiss and cutthroat trout O. clarki. Longitudinal arrangements of two- and six-antennas allow determination of direction of movement and efficiency of detection. Our first detector system became operational in August 2001, with subsequent improvements over time. In tests with a two-antenna system, detection efficiency of tagged, downstreammoving fish was high (96%) during low flows, but less (69%) during high flows. With an increase in the number of antennas to six, arranged in a 2x3 array, the detection efficiency of downstream-moving fish was increased to 95-100% at all flows. Detection efficiency of upstream-moving fish was high (95-100%) in both the two-and six-antenna system during all flows. Antennas were anchored to the substrate and largely spanned the bank-full width. Modifications to the methods used to anchor antennas have increased the likelihood of the system remaining intact and running at full detection capability during challenging flow and debris conditions, largely achieving our goal to have continuous monitoring of fish movement throughout an annual cycle. In August 2004, we placed a similar detector system in another watershed. Success has much relied on the quality of transceivers and electrical power. Detection of tagged fish passing our static PIT-tag detectors has produced valuable information on how selected fish species use the network of streams in a watershed. Integrating information from our detectors in tributary streams with that from detectors downstream at dams in the Columbia River has promise to be a powerful tool for monitoring movement patterns of anadromous fish species and to understanding full lifecycle fish behavior and habitat use.

Overview of fish immune system and infectious diseases

USDA-ARS?s Scientific Manuscript database

A brief overview of the fish immune system and the emerging or re-emerging bacterial, viral, parasitic and fungal diseases considered to currently have a negative impact on aquaculture is presented. The fish immune system has evolved with both innate (natural resistance) and adaptive (acquired) immu...

Influence of the Cholinergic System on the Immune Response of Teleost Fishes: Potential Model in Biomedical Research

PubMed Central

Toledo-Ibarra, G. A.; Rojas-Mayorquín, A. E.; Girón-Pérez, M. I.

2013-01-01

Fishes are the phylogenetically oldest vertebrate group, which includes more than one-half of the vertebrates on the planet; additionally, many species have ecological and economic importance. Fish are the first evolved group of organisms with adaptive immune mechanisms; consequently, they are an important link in the evolution of the immune system, thus a potential model for understanding the mechanisms of immunoregulation. Currently, the influence of the neurotransmitter acetylcholine (ACh) on the cells of the immune system is widely studied in mammalian models, which have provided evidence on ACh production by immune cells (the noncholinergic neuronal system); however, these neuroimmunomodulation mechanisms in fish and lower vertebrates are poorly studied. Therefore, the objective of this review paper was to analyze the influence of the cholinergic system on the immune response of teleost fish, which could provide information concerning the possibility of bidirectional communication between the nervous and immune systems in these organisms and provide data for a better understanding of basic issues in neuroimmunology in lower vertebrates, such as bony fishes. Thus, the use of fish as a model in biomedical research may contribute to a better understanding of human diseases and diseases in other animals. PMID:24324508

Influence of the cholinergic system on the immune response of teleost fishes: potential model in biomedical research.

PubMed

Toledo-Ibarra, G A; Rojas-Mayorquín, A E; Girón-Pérez, M I

2013-01-01

Fishes are the phylogenetically oldest vertebrate group, which includes more than one-half of the vertebrates on the planet; additionally, many species have ecological and economic importance. Fish are the first evolved group of organisms with adaptive immune mechanisms; consequently, they are an important link in the evolution of the immune system, thus a potential model for understanding the mechanisms of immunoregulation. Currently, the influence of the neurotransmitter acetylcholine (ACh) on the cells of the immune system is widely studied in mammalian models, which have provided evidence on ACh production by immune cells (the noncholinergic neuronal system); however, these neuroimmunomodulation mechanisms in fish and lower vertebrates are poorly studied. Therefore, the objective of this review paper was to analyze the influence of the cholinergic system on the immune response of teleost fish, which could provide information concerning the possibility of bidirectional communication between the nervous and immune systems in these organisms and provide data for a better understanding of basic issues in neuroimmunology in lower vertebrates, such as bony fishes. Thus, the use of fish as a model in biomedical research may contribute to a better understanding of human diseases and diseases in other animals.

Sperm motility in fish: technical applications and perspectives through CASA-Mot systems.

PubMed

Gallego, V; Asturiano, J F

2018-03-09

Although a relatively high number of sperm quality biomarkers have been reported over the years in several fish species, sperm motility is nowadays considered the best biomarker for fish spermatozoa. The first scientific reports focusing on fish sperm motility date from a century ago, but the objective assessment allowed by computer-aided sperm analysis (CASA-Mot) systems was not applied to fish species until the mid-1980s. Since then, a high number of sperm kinetic parameters from more than 170 fish species have been reported in more than 700 scientific articles, covering a wide range of topics, such as sperm physiology, sperm storage, broodstock management, the phenomenon of sperm competition, ecotoxicology and understanding the life cycle of the species. The sperm kinetic parameters provided by CASA-Mot systems can serve as powerful and useful tools for aquaculture and ecological purposes, and this review provides an overview of the major research areas in which fish sperm motility assessment by a CASA-Mot system has been used successfully.

An All-Fiber-Optic Combined System of Noncontact Photoacoustic Tomography and Optical Coherence Tomography

PubMed Central

Eom, Jonghyun; Shin, Jun Geun; Park, Soongho; Rim, Sunghwan; Lee, Byeong Ha

2016-01-01

We propose an all-fiber-based dual-modal imaging system that combines noncontact photoacoustic tomography (PAT) and optical coherence tomography (OCT). The PAT remotely measures photoacoustic (PA) signals with a 1550-nm laser on the surface of a sample by utilizing a fiber interferometer as an ultrasound detector. The fiber-based OCT, employing a swept-source laser centered at 1310 nm, shares the sample arm of the PAT system. The fiber-optic probe for the combined system was homemade with a lensed single-mode fiber (SMF) and a large-core multimode fiber (MMF). The compact and robust common probe is capable of obtaining both the PA and the OCT signals at the same position without any physical contact. Additionally, the MMF of the probe delivers the short pulses of a Nd:YAG laser to efficiently excite the PA signals. We experimentally demonstrate the feasibility of the proposed dual-modal system with a phantom made of a fishing line and a black polyethylene terephthalate fiber in a tissue mimicking solution. The all-fiber-optic system, capable of providing complementary information about absorption and scattering, has a promising potential in minimally invasive and endoscopic imaging. PMID:27213392

An All-Fiber-Optic Combined System of Noncontact Photoacoustic Tomography and Optical Coherence Tomography.

PubMed

Eom, Jonghyun; Shin, Jun Geun; Park, Soongho; Rim, Sunghwan; Lee, Byeong Ha

2016-05-20

We propose an all-fiber-based dual-modal imaging system that combines noncontact photoacoustic tomography (PAT) and optical coherence tomography (OCT). The PAT remotely measures photoacoustic (PA) signals with a 1550-nm laser on the surface of a sample by utilizing a fiber interferometer as an ultrasound detector. The fiber-based OCT, employing a swept-source laser centered at 1310 nm, shares the sample arm of the PAT system. The fiber-optic probe for the combined system was homemade with a lensed single-mode fiber (SMF) and a large-core multimode fiber (MMF). The compact and robust common probe is capable of obtaining both the PA and the OCT signals at the same position without any physical contact. Additionally, the MMF of the probe delivers the short pulses of a Nd:YAG laser to efficiently excite the PA signals. We experimentally demonstrate the feasibility of the proposed dual-modal system with a phantom made of a fishing line and a black polyethylene terephthalate fiber in a tissue mimicking solution. The all-fiber-optic system, capable of providing complementary information about absorption and scattering, has a promising potential in minimally invasive and endoscopic imaging.

Hydrodynamic studies on two wiggling hydrofoils in an oblique arrangement

NASA Astrophysics Data System (ADS)

Lin, Xingjian; He, Guoyi; He, Xinyi; Wang, Qi; Chen, Longsheng

2018-06-01

The propulsive performance of an oblique school of fish is numerically studied using an immersed boundary technique. The effect of the spacing and wiggling phase on the hydrodynamics of the system is investigated. The hydrodynamics of the system is deeply affected by the spacing between each fish in the school. When the horizontal separation is smaller than the length of the fish body, the downstream fish exhibits a larger thrust coefficient and greater propulsive efficiency than the isolated fish. However, the corresponding values for the upstream fish are smaller. The opposite behavior occurs when the horizontal separation increases beyond the length of fish body. The propulsive performance of the entire oblique school of fish can be substantially enhanced when the separations are optimized.

Neural processing, perception, and behavioral responses to natural chemical stimuli by fish and crustaceans.

PubMed

Derby, Charles D; Sorensen, Peter W

2008-07-01

This manuscript reviews the chemical ecology of two of the major aquatic animal models, fish and crustaceans, in the study of chemoreception. By necessity, it is restricted in scope, with most emphasis placed on teleost fish and decapod crustaceans. First, we describe the nature of the chemical world perceived by fish and crustaceans, giving examples of the abilities of these animals to analyze complex natural odors. Fish and crustaceans share the same environments and have evolved some similar chemosensory features: the ability to detect and discern mixtures of small metabolites in highly variable backgrounds and to use this information to identify food, mates, predators, and habitat. Next, we give examples of the molecular nature of some of these natural products, including a description of methodologies used to identify them. Both fish and crustaceans use their olfactory and gustatory systems to detect amino acids, amines, and nucleotides, among many other compounds, while fish olfactory systems also detect mixtures of sex steroids and prostaglandins with high specificity and sensitivity. Third, we discuss the importance of plasticity in chemical sensing by fish and crustaceans. Finally, we conclude with a description of how natural chemical stimuli are processed by chemosensory systems. In both fishes and crustaceans, the olfactory system is especially adept at mixture discrimination, while gustation is well suited to facilitate precise localization and ingestion of food. The behaviors of both fish and crustaceans can be defined by the chemical worlds in which they live and the abilities of their nervous systems to detect and identify specific features in their domains. An understanding of these worlds and the sensory systems that provide the animals with information about them provides insight into the chemical ecology of these species.

Neuroanatomical organization of the cholinergic system in the central nervous system of a basal actinopterygian fish, the senegal bichir Polypterus senegalus.

PubMed

López, Jesús M; Perlado, Jorge; Morona, Ruth; Northcutt, R Glenn; González, Agustín

2013-01-01

Polypterid bony fishes are believed to be basal to other living ray-finned fishes, and their brain organization is therefore critical in providing information as to primitive neural characters that existed in the earliest ray-finned fishes. The cholinergic system has been characterized in more advanced ray-finned fishes, but not in polypterids. In order to establish which cholinergic neural centers characterized the earliest ray-finned fishes, the distribution of choline acetyltransferase (ChAT) is described in Polypterus and compared with the distribution of this molecule in other ray-finned fishes. Cell groups immunoreactive for ChAT were observed in the hypothalamus, the habenula, the optic tectum, the isthmus, the cranial motor nuclei, and the spinal motor column. Cholinergic fibers were observed in both the telencephalic pallium and the subpallium, in the thalamus and pretectum, in the optic tectum and torus semicircularis, in the mesencephalic tegmentum, in the cerebellar crest, in the solitary nucleus, and in the dorsal column nuclei. Comparison of the data within a segmental neuromeric context indicates that the cholinergic system in polypterid fishes is generally similar to that in other ray-finned fishes, but cholinergic-positive neurons in the pallium and subpallium, and in the thalamus and cerebellum, of teleosts appear to have evolved following the separation of polypterids and other ray-finned fishes. Copyright © 2012 Wiley Periodicals, Inc.

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.

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.

Analysis of HER2 status in breast carcinoma by fully automated HER2 fluorescence in situ hybridization (FISH): comparison of two immunohistochemical tests and manual FISH.

PubMed

Yoon, Nara; Do, In-Gu; Cho, Eun Yoon

2014-09-01

Easy and accurate HER2 testing is essential when considering the prognostic and predictive significance of HER2 in breast cancer. The use of a fully automated, quantitative FISH assay would be helpful to detect HER2 amplification in breast cancer tissue specimens with reduced inter-laboratory variability. We compared the concordance of HER2 status as assessed by an automated FISH staining system to manual FISH testing. Using 60 formalin-fixed paraffin-embedded breast carcinoma specimens, we assessed HER2 immunoexpression with two antibodies (DAKO HercepTest and CB11). In addition, HER2 status was evaluated with automated FISH using the Leica FISH System for BOND and a manual FISH using the Abbott PathVysion DNA Probe Kit. All but one specimen were successfully stained using both FISH methods. When the data were divided into two groups according to HER2/CEP17 ratio, positive and negative, the results from both the automated and manual FISH techniques were identical for all 59 evaluable specimens. The HER2 and CEP17 copy numbers and HER2/CEP17 ratio showed great agreement between both FISH methods. The automated FISH technique was interpretable with signal intensity similar to those of the manual FISH technique. In contrast with manual FISH, the automated FISH technique showed well-preserved architecture due to low membrane digestion. HER2 immunohistochemistry and FISH results showed substantial significant agreement (κ = 1.0, p < 0.001). HER2 status can be reliably determined using a fully automated HER2 FISH system with high concordance to the well-established manual FISH method. Because of stable signal intensity and high staining quality, the automated FISH technique may be more appropriate than manual FISH for routine applications. © 2013 APMIS. Published by John Wiley & Sons Ltd.

Trematode Metacercariae in Freshwater Fish from Water Systems of Hantangang and Imjingang in Republic of Korea

PubMed Central

Sohn, Woon-Mok; Na, Byoung-Kuk; Cho, Shin-Hyeong; Lee, Soon-Won; Choi, Seung-Bong; Seok, Won-Seok

2015-01-01

The infection status of freshwater fish with digenetic trematode metacercariae was examined in water systems of Hantangang and Imjingang (River), the Republic of Korea. A total of 877 (594 from Hantangang and 283 from Imjingang) fishes were examined by the artificial digestion methods. Clonorchis sinensis metacercariae were detected in 7 (1.2%) fishes (in 3 spp.) from Hantangang in Cheorwon-gun, Gangwon-do, and 40 (14.1%) fishes (in 7 spp.) from Munsancheon in Paju-si, Gyeonggi-do. The average densities were 1.9 and 35.6 per fish infected, respectively. Metagonimus spp. metacercariae were detected in 312 (52.5%) and 113 (39.9%) fishes from Hantangang and Imjingang, and their average densities were 47.5 and 9.6 per fish infected, respectively. Centrocestus armatus metacercariae were found in 161 (27.1%) and 70 (24.7%) fishes from Hantangang and Imjingang, and their average number per fish infected was 694 and 82, respectively. Echinostoma spp. metacercariae were detected in 50 (8.4%) and 94 (33.2%) fishes from Hantangang and Imjingang, and their average densities were 9.6 and 23.1 per fish infected, respectively. The infection status of fishes with metacercariae of Stephanoprora spp., Diplostomum spp., Clinostomum complanatum, Metorchis orientalis, and Metorchis taiwanensis were analyzed by surveyed regions. Conclusively, it was confirmed that C. sinensis metacercariae were quite commonly detected in fishes from Munsancheon but rarely from other localities, whereas the metacercariae of other digenetic trematodes were relatively prevalent in fishes from water systems of Hantangang and Imjingang in Korea. PMID:26174822

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.

Invasive fishes generate biogeochemical hotspots in a nutrient-limited system.

PubMed

Capps, Krista A; Flecker, Alexander S

2013-01-01

Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems.

Invasive Fishes Generate Biogeochemical Hotspots in a Nutrient-Limited System

PubMed Central

Capps, Krista A.; Flecker, Alexander S.

2013-01-01

Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems. PMID:23342083

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.

Bessel light sheet structured illumination microscopy

NASA Astrophysics Data System (ADS)

Noshirvani Allahabadi, Golchehr

Biomedical study researchers using animals to model disease and treatment need fast, deep, noninvasive, and inexpensive multi-channel imaging methods. Traditional fluorescence microscopy meets those criteria to an extent. Specifically, two-photon and confocal microscopy, the two most commonly used methods, are limited in penetration depth, cost, resolution, and field of view. In addition, two-photon microscopy has limited ability in multi-channel imaging. Light sheet microscopy, a fast developing 3D fluorescence imaging method, offers attractive advantages over traditional two-photon and confocal microscopy. Light sheet microscopy is much more applicable for in vivo 3D time-lapsed imaging, owing to its selective illumination of tissue layer, superior speed, low light exposure, high penetration depth, and low levels of photobleaching. However, standard light sheet microscopy using Gaussian beam excitation has two main disadvantages: 1) the field of view (FOV) of light sheet microscopy is limited by the depth of focus of the Gaussian beam. 2) Light-sheet images can be degraded by scattering, which limits the penetration of the excitation beam and blurs emission images in deep tissue layers. While two-sided sheet illumination, which doubles the field of view by illuminating the sample from opposite sides, offers a potential solution, the technique adds complexity and cost to the imaging system. We investigate a new technique to address these limitations: Bessel light sheet microscopy in combination with incoherent nonlinear Structured Illumination Microscopy (SIM). Results demonstrate that, at visible wavelengths, Bessel excitation penetrates up to 250 microns deep in the scattering media with single-side illumination. Bessel light sheet microscope achieves confocal level resolution at a lateral resolution of 0.3 micron and an axial resolution of 1 micron. Incoherent nonlinear SIM further reduces the diffused background in Bessel light sheet images, resulting in confocal quality images in thick tissue. The technique was applied to live transgenic zebra fish tg(kdrl:GFP), and the sub-cellular structure of fish vasculature genetically labeled with GFP was captured in 3D. The superior speed of the microscope enables us to acquire signal from 200 layers of a thick sample in 4 minutes. The compact microscope uses exclusively off-the-shelf components and offers a low-cost imaging solution for studying small animal models or tissue samples.

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.

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 .

Ecological mechanisms underlying the sustainability of the agricultural heritage rice-fish coculture system.

PubMed

Xie, Jian; Hu, Liangliang; Tang, Jianjun; Wu, Xue; Li, Nana; Yuan, Yongge; Yang, Haishui; Zhang, Jiaen; Luo, Shiming; Chen, Xin

2011-12-13

For centuries, traditional agricultural systems have contributed to food and livelihood security throughout the world. Recognizing the ecological legacy in the traditional agricultural systems may help us develop novel sustainable agriculture. We examine how rice-fish coculture (RF), which has been designated a "globally important agricultural heritage system," has been maintained for over 1,200 y in south China. A field survey demonstrated that although rice yield and rice-yield stability are similar in RF and rice monoculture (RM), RF requires 68% less pesticide and 24% less chemical fertilizer than RM. A field experiment confirmed this result. We documented that a mutually beneficial relationship between rice and fish develops in RF: Fish reduce rice pests and rice favors fish by moderating the water environment. This positive relationship between rice and fish reduces the need for pesticides in RF. Our results also indicate a complementary use of nitrogen (N) between rice and fish in RF, resulting in low N fertilizer application and low N release into the environment. These findings provide unique insights into how positive interactions and complementary use of resource between species generate emergent ecosystem properties and how modern agricultural systems might be improved by exploiting synergies between species.

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.

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.

Resolution of fine biological structure including small narcomedusae across a front in the Southern California Bight

NASA Astrophysics Data System (ADS)

McClatchie, Sam; Cowen, Robert; Nieto, Karen; Greer, Adam; Luo, Jessica Y.; Guigand, Cedric; Demer, David; Griffith, David; Rudnick, Daniel

2012-04-01

We sampled a front detected by SST gradient, ocean color imagery, and a Spray glider south of San Nicolas Island in the Southern California Bight between 14 and 18 October 2010. We sampled the front with an unusually extensive array of instrumentation, including the Continuous Underway Fish Egg Sampler (CUFES), the undulating In Situ Ichthyoplankton Imaging System (ISIIS) (fitted with temperature, salinity, oxygen, and fluorescence sensors), multifrequency acoustics, a surface pelagic trawl, a bongo net, and a neuston net. We found higher fluorescence and greater cladoceran, decapod, and euphausiid densities in the front, indicating increased primary and secondary production. Mesopelagic fish were most abundant in oceanic waters to the west of the front, market squid were abundant in the front associated with higher krill and decapod densities, and jack mackerel were most common in the front and on the shoreward side of the front. Egg densities peaked to either side of the front, consistent with both offshore (for oceanic squid and mesopelagic fish) and shelf origins (for white croaker and California halibut). We discovered unusually high concentrations of predatory narcomedusae in the surface layer of the frontal zone. Potential ichthyoplankton predators were more abundant either in the front (decapods, euphausiids, and squid) or shoreward of the front (medusae, chaetognaths, and jack mackerel). For pelagic fish like sardine, which can thrive in less productive waters, the safest place to spawn would be offshore because there are fewer potential predators.

Visual Equivalence and Amodal Completion in Cuttlefish

PubMed Central

Lin, I-Rong; Chiao, Chuan-Chin

2017-01-01

Modern cephalopods are notably the most intelligent invertebrates and this is accompanied by keen vision. Despite extensive studies investigating the visual systems of cephalopods, little is known about their visual perception and object recognition. In the present study, we investigated the visual processing of the cuttlefish Sepia pharaonis, including visual equivalence and amodal completion. Cuttlefish were trained to discriminate images of shrimp and fish using the operant conditioning paradigm. After cuttlefish reached the learning criteria, a series of discrimination tasks were conducted. In the visual equivalence experiment, several transformed versions of the training images, such as images reduced in size, images reduced in contrast, sketches of the images, the contours of the images, and silhouettes of the images, were used. In the amodal completion experiment, partially occluded views of the original images were used. The results showed that cuttlefish were able to treat the training images of reduced size and sketches as the visual equivalence. Cuttlefish were also capable of recognizing partially occluded versions of the training image. Furthermore, individual differences in performance suggest that some cuttlefish may be able to recognize objects when visual information was partly removed. These findings support the hypothesis that the visual perception of cuttlefish involves both visual equivalence and amodal completion. The results from this research also provide insights into the visual processing mechanisms used by cephalopods. PMID:28220075

Georeferencing the Large-Scale Aerial Photographs of a Great Lakes Coastal Wetland: A Modified Photogrammetric Method

USGS Publications Warehouse

Murphy, Marilyn K.; Kowalski, Kurt P.; Grapentine, Joel L.

2010-01-01

The geocontrol template method was developed to georeference multiple, overlapping analog aerial photographs without reliance upon conventionally obtained horizontal ground control. The method was tested as part of a long-term wetland habitat restoration project at a Lake Erie coastal wetland complex in the U.S. Fish and Wildlife Service Ottawa National Wildlife Refuge. As in most coastal wetlands, annually identifiable ground-control features required to georeference photo-interpreted data are difficult to find. The geocontrol template method relies on the following four components: (a) an uncontrolled aerial photo mosaic of the study area, (b) global positioning system (GPS) derived horizontal coordinates of each photo’s principal point, (c) a geocontrol template created by the transfer of fiducial markings and calculated principal points to clear acetate from individual photographs arranged in a mosaic, and (d) the root-mean-square-error testing of the system to ensure an acceptable level of planimetric accuracy. Once created for a study area, the geocontrol template can be registered in geographic information system (GIS) software to facilitate interpretation of multiple images without individual image registration. The geocontrol template enables precise georeferencing of single images within larger blocks of photographs using a repeatable and consistent method.

Influence of the Enteric Nervous System on Gut Motility Patterns in Zebrafish

NASA Astrophysics Data System (ADS)

Baker, Ryan; Ganz, Julia; Melancon, Ellie; Eisen, Judith; Parthasarathy, Raghuveer

The enteric nervous system (ENS), composed of diverse neuronal subtypes and glia, regulates essential gut functions including motility, secretion, and homeostasis. In humans and animals, decreased numbers of enteric neurons lead to a variety of types of gut dysfunction. However, surprisingly little is known about how the number, position, or subtype of enteric neurons affect the regulation of gut peristalsis, due to the lack of good model systems and the lack of tools for the quantitative characterization of gut motion. We have therefore developed a method of quantitative spatiotemporal mapping using differential interference contrast microscopy and particle image velocimetry, and have applied this to investigate intestinal dynamics in normal and mutant larval zebrafish. From movies of gut motility, we obtain a velocity vector field representative of gut motion, from which we can quantify parameters relating to gut peristalsis such as frequency, wave speed, deformation amplitudes, wave duration, and non-linearity of waves. We show that mutants with reduced neuron number have contractions that are more regular in time and reduced in amplitude compared to wild-type (normal) fish. We also show that feeding fish before their yolk is consumed leads to stronger motility patterns. We acknowledge support from NIH awards P50 GM098911 and P01 HD022486.

Mechanisms driving recruitment variability in fish: comparisons between the Laurentian Great Lakes and marine systems

USGS Publications Warehouse

Pritt, Jeremy J.; Roseman, Edward F.; O'Brien, Timothy P.

2014-01-01

In his seminal work, Hjort (in Fluctuations in the great fisheries of Northern Europe. Conseil Parmanent International Pour L'Exploration De La Mar. Rapports et Proces-Verbaux, 20: 1–228, 1914) observed that fish population levels fluctuated widely, year-class strength was set early in life, and egg production by adults could not alone explain variability in year-class strength. These observations laid the foundation for hypotheses on mechanisms driving recruitment variability in marine systems. More recently, researchers have sought to explain year-class strength of important fish in the Laurentian Great Lakes and some of the hypotheses developed for marine fisheries have been transferred to Great Lakes fish. We conducted a literature review to determine the applicability of marine recruitment hypotheses to Great Lakes fish. We found that temperature, interspecific interactions, and spawner effects (abundance, age, and condition of adults) were the most important factors in explaining recruitment variability in Great Lakes fish, whereas relatively fewer studies identified bottom-up trophodynamic factors or hydrodynamic factors as important. Next, we compared recruitment between Great Lakes and Baltic Sea fish populations and found no statistical difference in factors driving recruitment between the two systems, indicating that recruitment hypotheses may often be transferable between Great Lakes and marine systems. Many recruitment hypotheses developed for marine fish have yet to be applied to Great Lakes fish. We suggest that future research on recruitment in the Great Lakes should focus on forecasting the effects of climate change and invasive species. Further, because the Great Lakes are smaller and more enclosed than marine systems, and have abundant fishery-independent data, they are excellent candidates for future hypothesis testing on recruitment in fish.

The hypothalamic-pituitary-thyroid (HPT) axis in fish and its role in fish development and reproduction.

PubMed

Blanton, Michael L; Specker, Jennifer L

2007-01-01

Bony fishes represent the largest vertebrate class and are a very diverse animal group. This chapter provides a thorough review of the available scientific literature on the thyroid system in these important vertebrate animals. The molecular components of the hypothalamic-pituitary-thyroid (HPT) axis in this group correspond closely to those of mammals. The thyroid tissue in the fishes is organized as diffuse follicles, with a few exceptions, rather than as an encapsulated gland as is found in most other vertebrate species. The features of this diffuse tissue in fishes are reviewed with an emphasis on feedback relationships within the HPT axis, the molecular biology of the thyroid system in fishes, and comparisons versus the thyroid systems of other vertebrate taxa. A review of the role of thyroid hormone in fish development and reproduction is included. Available information about the HPT axis in fishes is quite detailed for some species and rather limited or absent in others. This review focuses on species that have been intensively studied for their value as laboratory models in assays to investigate disruption in normal function of the thyroid system. In addition, in vitro and in vivo assay methods for screening chemicals for their potential to interfere with the thyroid system are reviewed. It is concluded that there are currently no in vitro or in vivo assays in fish species that are sufficiently developed to warrant recommendation for use to efficiently screen chemicals for thyroid disruption. Methods are available that can be used to measure thyroid hormones, although our ability to interpret the causes and implications of potential alterations in T4 or T3 levels in fishes is nonetheless limited without further research.

Multimodal in vivo blood flow sensing combining particle image velocimetry and optical tweezers-based blood steering

NASA Astrophysics Data System (ADS)

Meissner, Robert; Sugden, Wade W.; Siekmann, Arndt F.; Denz, Cornelia

2018-02-01

All higher developed organisms contain complex hierarchical networks of arteries, veins and capillaries. These constitute the cardiovascular system responsible for supplying nutrients, gas and waste exchange. Diseases related to the cardiovascular system are among the main causes for death worldwide. In order to understand the processes leading to arteriovenous malformation, we studied hereditary hemorrhagic telangiectasia (HHT), which has a prevalence of 1:5000 worldwide and causes internal bleeding. In zebrafish, HHT is induced by mutation of the endoglin gene involved in HHT and observed to reduce red blood cell (RBC) flow to intersegmental vessels (ISVs) in the tail due to malformations of the dorsal aorta (DA) and posterior cardinal vein (PCV). However, these capillaries are still functional. Changes in the blood flow pattern are observed from in vivo data from zebrafish embryos through particle image velocimetry (PIV). Wall shear rates (WSRs) and blood flow velocities are obtained non-invasively with millisecond resolution. We observe significant increases of blood flow velocity in the DA for endoglin-deficient zebrafish embryos (mutants) at 3 days post fertilization. In the PCV, this increase is even more pronounced. We identified an increased similarity between the DA and the PCV of mutant fish compared to siblings, i.e., unaffected fish. To counteract the reduced RBC flow to ISVs we implement optical tweezers (OT). RBCs are steered into previously unperfused ISVs showing a significant increase of RBC count per minute. We discuss limitations with respect to biocompatibility of optical tweezers in vivo and determination of in vivo wall shear stress (WSS) connected to normal and endoglin-deficicent zebrafish embryos.

Functional characterization of neotropical snakes peripheral blood leukocytes subsets: Linking flow cytometry cell features, microscopy images and serum corticosterone levels.

PubMed

de Carvalho, Marcelo Pires Nogueira; Queiroz-Hazarbassanov, Nicolle Gilda Teixeira; de Oliveira Massoco, Cristina; Sant'Anna, Sávio Stefanini; Lourenço, Mariana Mathias; Levin, Gabriel; Sogayar, Mari Cleide; Grego, Kathleen Fernandes; Catão-Dias, José Luiz

2017-09-01

Reptiles are the unique ectothermic amniotes, providing the key link between ectothermic anamniotes fish and amphibians, and endothermic birds and mammals; becoming an important group to study with the aim of providing significant knowledge into the evolutionary history of vertebrate immunity. Classification systems for reptiles' leukocytes have been described by their appearance rather than function, being still inconsistent. With the advent of modern techniques and the establishment of analytical protocols for snakes' blood by flow cytometry, we bring a qualitative and quantitative assessment of innate activities presented by snakes' peripheral blood leukocytes, thereby linking flow cytometric features with fluorescent and light microscopy images. Moreover, since corticosterone is an important immunomodulator in reptiles, hormone levels of all blood samples were measured. We provide novel and additional information which should contribute to better understanding of the development of the immune system of reptiles and vertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Columbia River System Operation Review : Final Environmental Impact Statement, Appendix C: Anadromous Fish and Juvenile Fish Transportation.

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

Columbia River System Operation Review

1995-11-01

This Appendix C of the Final Environmental Impact Statement for the Columbia River System discusses impacts on andromous fish and juvenile fish transportation. The principal andromous fish in the Columbia basin include salmonid species (Chinook, coho, and sockeye salmon, and steelhead) and nonsalmoinid andromous species (sturgeon, lamprey, and shad). Major sections in this document include the following: background, scope and process; affected environment for salmon and steelhead, shaded, lamprey, sturgeon; study methods; description of alternatives: qualitative and quantitative findings.

Spinoff 2009

NASA Technical Reports Server (NTRS)

2009-01-01

Topics covered include: Image-Capture Devices Extend Medicine's Reach; Medical Devices Assess, Treat Balance Disorders; NASA Bioreactors Advance Disease Treatments; Robotics Algorithms Provide Nutritional Guidelines; "Anti-Gravity" Treadmills Speed Rehabilitation; Crew Management Processes Revitalize Patient Care; Hubble Systems Optimize Hospital Schedules; Web-based Programs Assess Cognitive Fitness; Electrolyte Concentrates Treat Dehydration; Tools Lighten Designs, Maintain Structural Integrity; Insulating Foams Save Money, Increase Safety; Polyimide Resins Resist Extreme Temperatures; Sensors Locate Radio Interference; Surface Operations Systems Improve Airport Efficiency; Nontoxic Resins Advance Aerospace Manufacturing; Sensors Provide Early Warning of Biological Threats; Robot Saves Soldier's Lives Overseas (MarcBot); Apollo-Era Life Raft Saves Hundreds of Sailors; Circuits Enhance Scientific Instruments and Safety Devices; Tough Textiles Protect Payloads and Public Safety Officers; Forecasting Tools Point to Fishing Hotspots; Air Purifiers Eliminate Pathogens, Preserve Food; Fabrics Protect Sensitive Skin from UV Rays; Phase Change Fabrics Control Temperature; Tiny Devices Project Sharp, Colorful Images; Star-Mapping Tools Enable Tracking of Endangered Animals; Nanofiber Filters Eliminate Contaminants; Modeling Innovations Advance Wind Energy Industry; Thermal Insulation Strips Conserve Energy; Satellite Respondent Buoys Identify Ocean Debris; Mobile Instruments Measure Atmospheric Pollutants; Cloud Imagers Offer New Details on Earth's Health; Antennas Lower Cost of Satellite Access; Feature Detection Systems Enhance Satellite Imagery; Chlorophyll Meters Aid Plant Nutrient Management; Telemetry Boards Interpret Rocket, Airplane Engine Data; Programs Automate Complex Operations Monitoring; Software Tools Streamline Project Management; Modeling Languages Refine Vehicle Design; Radio Relays Improve Wireless Products; Advanced Sensors Boost Optical Communication, Imaging; Tensile Fabrics Enhance Architecture Around the World; Robust Light Filters Support Powerful Imaging Devices; Thermoelectric Devices Cool, Power Electronics; Innovative Tools Advance Revolutionary Weld Technique; Methods Reduce Cost, Enhance Quality of Nanotubes; Gauging Systems Monitor Cryogenic Liquids; Voltage Sensors Monitor Harmful Static; and Compact Instruments Measure Heat Potential.

Complete feeds-intensive systems

USDA-ARS?s Scientific Manuscript database

Most commercially cultivated fish are raised in high-density culture systems where the assumption is that the contribution of natural foods to the nutrition of the fish is insignificant. Thus, intensively cultured fish must be fed a nutritionally complete feed. A short section on the concept and im...

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.

A fast and flexible panoramic virtual reality system for behavioural and electrophysiological experiments.

PubMed

Takalo, Jouni; Piironen, Arto; Honkanen, Anna; Lempeä, Mikko; Aikio, Mika; Tuukkanen, Tuomas; Vähäsöyrinki, Mikko

2012-01-01

Ideally, neuronal functions would be studied by performing experiments with unconstrained animals whilst they behave in their natural environment. Although this is not feasible currently for most animal models, one can mimic the natural environment in the laboratory by using a virtual reality (VR) environment. Here we present a novel VR system based upon a spherical projection of computer generated images using a modified commercial data projector with an add-on fish-eye lens. This system provides equidistant visual stimulation with extensive coverage of the visual field, high spatio-temporal resolution and flexible stimulus generation using a standard computer. It also includes a track-ball system for closed-loop behavioural experiments with walking animals. We present a detailed description of the system and characterize it thoroughly. Finally, we demonstrate the VR system's performance whilst operating in closed-loop conditions by showing the movement trajectories of the cockroaches during exploratory behaviour in a VR forest.

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.

A novel system applying the 2-deoxyglucose method to fish for characterization of environmental neurotoxins.

PubMed

Choich, J A; Sass, J B; Silbergeld, E K

2002-01-01

Methods of identifying and preventing ecotoxicity related to environmental stressors on wildlife species are underdeveloped. To detect sublethal effects, we have devised a neurochemical method of evaluating environmental neurotoxins by a measuring changes in regional neural activity in the central nervous system of fish. Our system is a unique adaptation of the 2-deoxyglucose (2-DG) method originally developed by L. Sokoloff in 1977, which is based on the direct relationship between glucose metabolism and neural functioning at the regional level. We applied these concepts to test the assumption that changes in neural activity as a result of chemical exposure would produce measurable effects on the amount of [(14)C]2-DG accumulated regionally in the brain of Tilapia nilatica. For purposes of this study, we utilized the excitotoxin N-methyl-D-aspartate (NMDA) to characterize the response of the central nervous system. Regional accumulation of [(14)C]2-DG was visualized by autoradiography and digital image processing. Observable increases in regional [(14) C] 2-DG uptake were evident in all NMDA-treated groups as compared to controls. Specific areas of increased [(14)C] 2-DG uptake included the telencephalon, optic tectum, and regions of the cerebellum, all areas in which high concentrations of NMDA-subtype glutamate receptors have been found in Tilapia monsanbica. These results are consistent with the known neural excitatory action of NMDA.

Establishment and Usability Evaluation of an Interactive AR Learning System on Conservation of Fish

ERIC Educational Resources Information Center

Lin, Hao-Chiang Koong; Hsieh, Min-Chai; Wang, Cheng-Hung; Sie, Zong-Yuan; Chang, Shei-Hsi

2011-01-01

In this study, we develop an interactive AR Learning System based on Augmented Reality and interactive touch-screen. The learning content knowledge is about conservation of fish in Taiwan. The system combines the game by the concept of AR book which allows children to learn about the importance of conservation of fish. A mechanism is designed to…

Nonnative Fishes in the Upper Mississippi River System

USGS Publications Warehouse

Irons, Kevin S.; DeLain, Steven A.; Gittinger, Eric; Ickes, Brian S.; Kolar, Cindy S.; Ostendort, David; Ratcliff, Eric N.; Benson, Amy J.; Irons, Kevin S.

2009-01-01

The introduction, spread, and establishment of nonnative species is widely regarded as a leading threat to aquatic biodiversity and consequently is ranked among the most serious environmental problems facing the United States today. This report presents information on nonnative fish species observed by the Long Term Resource Monitoring Program on the Upper Mississippi River System a nexus of North American freshwater fish diversity for the Nation. The Long Term Resource Monitoring Program, as part of the U.S. Army Corps of Engineers' Environmental Management Plan, is the Nation's largest river monitoring program and stands as the primary source of standardized ecological information on the Upper Mississippi River System. The Long Term Resource Monitoring Program has been monitoring fish communities in six study areas on the Upper Mississippi River System since 1989. During this period, more than 3.5 million individual fish, consisting of 139 species, have been collected. Although fish monitoring activities of the Long Term Resource Monitoring Program focus principally on entire fish communities, data collected by the Program are useful for detecting and monitoring the establishment and spread of nonnative fish species within the Upper Mississippi River System Basin. Sixteen taxa of nonnative fishes, or hybrids thereof, have been observed by the Long Term Resource Monitoring Program since 1989, and several species are presently expanding their distribution and increasing in abundance. For example, in one of the six study areas monitored by the Long Term Resource Monitoring Program, the number of established nonnative species has increased from two to eight species in less than 10 years. Furthermore, contributions of those eight species can account for up to 60 percent of the total annual catch and greater than 80 percent of the observed biomass. These observations are critical because the Upper Mississippi River System stands as a nationally significant pathway for nonnative species expansion between the Mississippi River and the Great Lakes Basin. This report presents a synthesis of data on nonnative fish species observed during Long Term Resource Monitoring Program monitoring activities.

Elucidating fishing effects in a large-predator dominated system: The case of Darwin and Wolf Islands (Galápagos)

NASA Astrophysics Data System (ADS)

Ruiz, Diego J.; Banks, Stuart; Wolff, Matthias

2016-01-01

Fifty years of artisanal fishing history in Galápagos characterized by boom and bust of resources has changed the natural marine community structure close to fishing ports in the Galápagos Marine Reserve. Nonetheless, the remote Darwin and Wolf Islands are still in a "near natural state" harboring high species richness unique for the archipelago and high biomass. Marine life that aggregates to the pinnacles linked to the wider oceanic seascape makes them interesting and unique systems in terms of community structure and study of on-shore/offshore trophic interactions. Although > 200 km from local fishing ports the two islands also support an artisanal fishery targeting large demersal predators of high trophic levels. They are areas prioritized for conservation actions by Galápagos National Park, and local non-governmental organizations given their natural heritage importance, value to local fishers and revenue from dive tourism attracted by the promise of large marine predator aggregations such as sharks. Given that catch data upon which to base conservation recommendations is sparse it is difficult to accurately estimate present day fishing trends in Darwin and Wolf. We used a trophic steady-state model that connects benthic and pelagic communities to assess the potential effects of a change in fishing intensity in the two islands system. A predator-prey matrix was built using the Ecopath with Ecosim (EwE) software with total biomass estimated at 937 t km- 2. Large fish aggregations accounted for 19%, primary producers for 9.0% and non-fish (seabirds, marine mammals and sea turtles) for less than 0.1% of the total living biomass. The total system size in terms of overall flows was 16,652 t km- 2 year- 1, four times larger than a generic seamount model but smaller than that modeled for a Galápagos upwelling system based upon the western Bolivar Channel region. Consumption and respiration dominated the flows in the system (53.4 and 31.8% respectively). The Darwin and Wolf system shows a mature state, dominated by respiration, and top-down control via sharks and benthic predatory fish as the most important system compartments in terms of biomass. Model simulations suggest that heavy fishing pressure on top predators would greatly change the system's trophic structure. The nature of impacts depended on the types of gears simulated. Reduced natural predator densities through fishing exert strong direct and indirect influences on the system towards sea urchin-dominated benthos.

Nanodelivery Systems as New Tools for Immunostimulant or Vaccine Administration: Targeting the Fish Immune System

PubMed Central

Ji, Jie; Torrealba, Debora; Ruyra, Àngels; Roher, Nerea

2015-01-01

Fish disease treatments have progressed significantly over the last few years and have moved from the massive use of antibiotics to the development of vaccines mainly based on inactivated bacteria. Today, the incorporation of immunostimulants and antigens into nanomaterials provide us with new tools to enhance the performance of immunostimulation. Nanoparticles are dispersions or solid particles designed with specific physical properties (size, surface charge, or loading capacity), which allow controlled delivery and therefore improved targeting and stimulation of the immune system. The use of these nanodelivery platforms in fish is in the initial steps of development. Here we review the advances in the application of nanoparticles to fish disease prevention including: the type of biomaterial, the type of immunostimulant or vaccine loaded into the nanoparticles, and how they target the fish immune system. PMID:26492276

50 CFR 622.4 - Permits and fees.

Code of Federal Regulations, 2011 CFR

2011-10-01

... migratory pelagic fish. (B) South Atlantic coastal migratory pelagic fish. (C) Gulf reef fish. (D) South... regarding a limited access system for charter vessel/headboat permits for Gulf reef fish and Gulf coastal... headboat, respectively. (iv) If Federal regulations for Gulf reef fish in subparts A, B, or C of this part...

50 CFR 622.4 - Permits and fees.

Code of Federal Regulations, 2010 CFR

2010-10-01

... migratory pelagic fish. (B) South Atlantic coastal migratory pelagic fish. (C) Gulf reef fish. (D) South... regarding a limited access system for charter vessel/headboat permits for Gulf reef fish and Gulf coastal... headboat, respectively. (iv) If Federal regulations for Gulf reef fish in subparts A, B, or C of this part...

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

ETV Program Report: Big Fish Septage and High Strength Waste Water Treatment System

EPA Science Inventory

Verification testing of the Big Fish Environmental Septage and High Strength Wastewater Processing System for treatment of high-strength wastewater was conducted at the Big Fish facility in Charlevoix, Michigan. Testing was conducted over a 13-month period to address different c...

Automatic trajectory measurement of large numbers of crowded objects

NASA Astrophysics Data System (ADS)

Li, Hui; Liu, Ye; Chen, Yan Qiu

2013-06-01

Complex motion patterns of natural systems, such as fish schools, bird flocks, and cell groups, have attracted great attention from scientists for years. Trajectory measurement of individuals is vital for quantitative and high-throughput study of their collective behaviors. However, such data are rare mainly due to the challenges of detection and tracking of large numbers of objects with similar visual features and frequent occlusions. We present an automatic and effective framework to measure trajectories of large numbers of crowded oval-shaped objects, such as fish and cells. We first use a novel dual ellipse locator to detect the coarse position of each individual and then propose a variance minimization active contour method to obtain the optimal segmentation results. For tracking, cost matrix of assignment between consecutive frames is trainable via a random forest classifier with many spatial, texture, and shape features. The optimal trajectories are found for the whole image sequence by solving two linear assignment problems. We evaluate the proposed method on many challenging data sets.

Habitat used by juvenile lake sturgeon (Acipenser fulvescens) in the North Channel of the St. Clair River (Michigan, USA)

USGS Publications Warehouse

Boase, James C.; Manny, Bruce A.; Donald, Katherine A.L.; Kennedy, Gregory W.; Diana, James S.; Thomas, Michael V.; Chiotti, Justin A.

2014-01-01

Lake sturgeon (Acipenser fulvescens) occupy the St. Clair River, part of a channel connecting lakes Huron and Erie in the Laurentian Great Lakes. In the North Channel of the St. Clair River, juvenile lake sturgeon (3–7 years old and 582–793 mm in length) were studied to determine movement patterns and habitat usage. Fourteen juveniles were implanted with ultrasonic transmitters and tracked June–August of 2004, 2005 and 2006. Telemetry data, Geographic Information System software, side-scan sonar, video images of the river bottom, scuba diving, and benthic substrate samples were used to determine the extent and composition of habitats they occupied. Juvenile lake sturgeon habitat selection was strongly related to water depth. No fish were found in 700 mm in length selected sand and gravel areas mixed with zebra mussels and areas dominated by zebra mussels, while fish < 700 mm used these habitat types in proportion to their availability.

Dynamic behavior and deformation analysis of the fish cage system using mass-spring model

NASA Astrophysics Data System (ADS)

Lee, Chun Woo; Lee, Jihoon; Park, Subong

2015-06-01

Fish cage systems are influenced by various oceanic conditions, and the movements and deformation of the system by the external forces can affect the safety of the system itself, as well as the species of fish being cultivated. Structural durability of the system against environmental factors has been major concern for the marine aquaculture system. In this research, a mathematical model and a simulation method were presented for analyzing the performance of the large-scale fish cage system influenced by current and waves. The cage system consisted of netting, mooring ropes, floats, sinkers and floating collar. All the elements were modeled by use of the mass-spring model. The structures were divided into finite elements and mass points were placed at the mid-point of each element, and mass points were connected by springs without mass. Each mass point was applied to external and internal forces, and total force was calculated in every integration step. The computation method was applied to the dynamic simulation of the actual fish cage systems rigged with synthetic fiber and copper wire simultaneously influenced by current and waves. Here, we also tried to find a relevant ratio between buoyancy and sinking force of the fish cages. The simulation results provide improved understanding of the behavior of the structure and valuable information concerning optimum ratio of the buoyancy to sinking force according to current speeds.

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.

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

Orientation through chemo reception in fishes

NASA Technical Reports Server (NTRS)

Kleerekoper, H.

1972-01-01

A system designed to acquire and process data describing locomotor behavior of fish is described. Data are recorded in relation to the fish's response to olfactory stimuli. It was concluded that fish orientation is based on rheataxis or chemotropotaxis.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

PubMed

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. The database is available for free at http://mail.nbfgr.res.in/fbis/

Design and demonstration of a fish robot actuated by a SMA-driven actuation system

NASA Astrophysics Data System (ADS)

Le, Chan H.; Nguyen, Quang S.; Park, Hoon C.

2010-04-01

This paper presents a concept of a fish robot actuated by an SMA-based actuator. The bending-type actuator system is composed of a 0.1mm diameter SMA wire and a 0.5mm thick glass/epoxy strip. The SMA wire is installed to the bent composite strip. The actuator can produce about 200gf of blocking force and 3.5mm displacement at the center of the glass/epoxy strip. The bending motion of the actuator is converted into the tail-beat motion of a fish robot through a linkage system. The fish robot is evaluated by measuring the tail-beat angle, swimming speed and thrust produced by the fish robot. The tail-beat angle is about 20° and the maximum swimming speed is about 1.6cm/s. The measured thrust is about 0.4gf when the fish robot is operated at 0.9Hz.

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.

Test of salt marsh as a site of production and export of fish biomass with implications for impoundment management and restoration

USGS Publications Warehouse

Stevens, Philip W.

2002-01-01

Salt marshes are among the most productive ecosystems in the world, and although they are thought to enhance the productivity of open estuarine waters, the mechanism by which energy transfer occurs has been debated for decades. One possible mechanism is the transfer of saltmarsh production to estuarine waters by vagile fishes and invertebrates. Saltmarsh impoundments in the Indian River Lagoon, Florida, that have been reconnected to the estuary by culverts provide unique opportunities for studying marsh systems with respect to aquatic communities. The boundaries between salt marshes and the estuary are clearly defined by a system of dikes that confine fishes into a known area, and the exchange of aquatic organisms are restricted to culverts where they may be easily sampled. A multi-gear approach was used monthly to estimate fish standing stock, fish ingress/egress, and predation. Changes in saltmarsh fish abundance, and exchange with the estuary reflected the seasonal pattern of marsh flooding in the xv northern Indian River Lagoon system. During a six month period of marsh flooding, saltmarsh fishes had continuous access to marsh food resources. Piscivorous fishes regularly entered the marsh via creeks and ditches to prey upon marsh fishes, and piscivorous birds aggregated following major fish migrations to the marsh surface or to deep habitats. As water levels receded in winter, saltmarsh fishes concentrated into deep habitats and migration to the estuary ensued. The monthly estimates of fish standing stock, net fish ingress, and predation were used to develop a biomass budget to estimate annual production of fishes and the relative yield to predatory fish, birds, and direct migration to the estuary. Annual production of saltmarsh fishes was estimated to be 17.7 g·m-2 salt marsh, which falls within the range of previously reported values for estuarine fish communities. The relative yields were at least 21% to piscivorous fishes, 14% to piscivorous birds, and 32% to export. Annual export of fish biomass was 5.6 g fish·m-2 salt marsh, representing about 2% of saltmarsh primary production. Saltmarsh fishes convert marsh production to high quality vagile biomass (fishes concentrate energy, protein, and nutrients as body mass) and move this readily useable production to the estuary, providing an efficient link between salt marshes and estuarine predators.

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

Status and conservation of the fish fauna of the Alabama River system

USGS Publications Warehouse

Freeman, Mary C.; Irwin, E.R.; Burkhead, N.M.; Freeman, B.J.; Bart, H.L.; Rinne, John N.; Hughes, Robert M.; Calamusso, Bob

2005-01-01

The Alabama River system, comprising the Alabama, Coosa, and Tallapoosa subsystems, forms the eastern portion of the Mobile River drainage. Physiographic diversity and geologic history have fostered development in the Alabama River system of globally significant levels of aquatic faunal diversity and endemism. At least 184 fishes are native to the system, including at least 33 endemic species. During the past century, dam construction for hydropower generation and navigation resulted in 16 reservoirs that inundate 44% of the length of the Alabama River system main stems. This extensive physical and hydrologic alteration has affected the fish fauna in three major ways. Diadromous and migratory species have declined precipitously. Fish assemblages persisting downstream from large main-stem dams have been simplified by loss of species unable to cope with altered flow and water quality regimes. Fish populations persisting in the headwaters and in tributaries to the mainstem reservoirs are now isolated and subjected to effects of physical and chemical habitat degradation. Ten fishes in the Alabama River system (including seven endemic species) are federally listed as threatened or endangered. Regional experts consider at least 28 additional species to be vulnerable, threatened, or endangered with extinction. Conserving the Alabama River system fish fauna will require innovative dam management, protection of streams from effects of urbanization and water supply development, and control of alien species dispersal. Failure to manage aggressively for integrity of remaining unimpounded portions of the Alabama River system will result in reduced quality of natural resources for future generations, continued assemblage simplification, and species extinction.

Status and conservation of the fish fauna of the Alabama River system

USGS Publications Warehouse

Freeman, Mary C.; Irwin, E.R.; Burkhead, N.M.; Freeman, B.J.; Bart, H.L.

2005-01-01

The Alabama River system, comprising the Alabama, Coosa, and Tallapoosa subsystems, forms the eastern portion of the Mobile River drainage. Physiographic diversity and geologic history have fostered development in the Alabama River system of globally significant levels of aquatic faunal diversity and endemism. At least 184 fishes are native to the system, including at least 33 endemic species. During the past century, dam construction for hydropower generation and navigation resulted in 16 reservoirs that inundate 44% of the length of the Alabama River system main stems. This extensive physical and hydrologic alteration has affected the fish fauna in three major ways. Diadromous and migratory species have declined precipitously. Fish assemblages persisting downstream from large main-stem dams have been simplified by loss of species unable to cope with altered flow and water quality regimes. Fish populations persisting in the headwaters and in tributaries to the mainstem reservoirs are now isolated and subjected to effects of physical and chemical habitat degradation. Ten fishes in the Alabama River system (including seven endemic species) are federally listed as threatened or endangered. Regional experts consider at least 28 additional species to be vulnerable, threatened, or endangered with extinction. Conserving the Alabama River system fish fauna will require innovative dam management, protection of streams from effects of urbanization and water supply development, and control of alien species dispersal. Failure to manage aggressively for integrity of remaining unimpounded portions of the Alabama River system will result in reduced quality of natural resources for future generations, continued assemblage simplification, and species extinctions. ?? 2005 by the American Fisheries Society.

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.

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.

Accurate Identification of ALK Positive Lung Carcinoma Patients: Novel FDA-Cleared Automated Fluorescence In Situ Hybridization Scanning System and Ultrasensitive Immunohistochemistry

PubMed Central

Conde, Esther; Suárez-Gauthier, Ana; Benito, Amparo; Garrido, Pilar; García-Campelo, Rosario; Biscuola, Michele; Paz-Ares, Luis; Hardisson, David; de Castro, Javier; Camacho, M. Carmen; Rodriguez-Abreu, Delvys; Abdulkader, Ihab; Ramirez, Josep; Reguart, Noemí; Salido, Marta; Pijuán, Lara; Arriola, Edurne; Sanz, Julián; Folgueras, Victoria; Villanueva, Noemí; Gómez-Román, Javier; Hidalgo, Manuel; López-Ríos, Fernando

2014-01-01

Background Based on the excellent results of the clinical trials with ALK-inhibitors, the importance of accurately identifying ALK positive lung cancer has never been greater. However, there are increasing number of recent publications addressing discordances between FISH and IHC. The controversy is further fuelled by the different regulatory approvals. This situation prompted us to investigate two ALK IHC antibodies (using a novel ultrasensitive detection-amplification kit) and an automated ALK FISH scanning system (FDA-cleared) in a series of non-small cell lung cancer tumor samples. Methods Forty-seven ALK FISH-positive and 56 ALK FISH-negative NSCLC samples were studied. All specimens were screened for ALK expression by two IHC antibodies (clone 5A4 from Novocastra and clone D5F3 from Ventana) and for ALK rearrangement by FISH (Vysis ALK FISH break-apart kit), which was automatically captured and scored by using Bioview's automated scanning system. Results All positive cases with the IHC antibodies were FISH-positive. There was only one IHC-negative case with both antibodies which showed a FISH-positive result. The overall sensitivity and specificity of the IHC in comparison with FISH were 98% and 100%, respectively. Conclusions The specificity of these ultrasensitive IHC assays may obviate the need for FISH confirmation in positive IHC cases. However, the likelihood of false negative IHC results strengthens the case for FISH testing, at least in some situations. PMID:25248157

Engineering Support for the Development of a Submersible Fish Cage for Open Ocean Aquaculture

DTIC Science & Technology

2007-01-01

32 Appendix B: Feed Hose Buoy Components ................................................................. 33...ballasting systems (for test purposes) located in the upper rim section and airlift. Another component of the system includes a feed hose buoy used...to deliver pellets to fish in the cage while the system is submerged. Since the feed hose buoy was not critical in the development of the fish

When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs

PubMed Central

van Denderen, P. Daniel; van Kooten, Tobias; Rijnsdorp, Adriaan D.

2013-01-01

Bottom trawls are a globally used fishing gear that physically disturb the seabed and kill non-target organisms, including those that are food for the targeted fish species. There are indications that ensuing changes to the benthic invertebrate community may increase the availability of food and promote growth and even fisheries yield of target fish species. If and how this occurs is the subject of ongoing debate, with evidence both in favour and against. We model the effects of trawling on a simple ecosystem of benthivorous fish and two food populations (benthos), susceptible and resistant to trawling. We show that the ecosystem response to trawling depends on whether the abundance of benthos is top-down or bottom-up controlled. Fishing may result in higher fish abundance, higher (maximum sustainable) yield and increased persistence of fish when the benthos which is the best-quality fish food is also more resistant to trawling. These positive effects occur in bottom-up controlled systems and systems with limited impact of fish feeding on benthos, resembling bottom-up control. Fishing leads to lower yields and fish persistence in all configurations where susceptible benthos are more profitable prey. Our results highlight the importance of mechanistic ecosystem knowledge as a requirement for successful management. PMID:24004941

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...

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.

Ciguatera and scombroid fish poisoning in the United States.

PubMed

Pennotti, Radha; Scallan, Elaine; Backer, Lorraine; Thomas, Jerry; Angulo, Frederick J

2013-12-01

Ciguatera and scombroid fish poisonings are common causes of fish-related foodborne illness in the United States; however, existing surveillance systems underestimate the overall human health impact. This study aimed to describe existing data on ciguatera and scombroid fish poisonings from outbreak and poison control center reports and to estimate the overall number of ciguatera and scombroid fish-poisoning illnesses, hospitalizations, and deaths in the United States. We analyzed outbreak data from the Foodborne Disease Outbreak Surveillance Systems (FDOSS) from 2000 to 2007 and poison control center call data from the National Poison Data System (NPDS) from 2005 to 2009 for reports of ciguatera and scombroid fish poisonings. Using a statistical model with many inputs, we adjusted the outbreak data for undercounting due to underreporting and underdiagnosis to generate estimates. Underreporting and underdiagnosis multipliers were derived from the poison control call data and the published literature. Annually, an average of 15 ciguatera and 28 scombroid fish-poisoning outbreaks, involving a total of 60 and 108 ill persons, respectively, were reported to FDOSS (2000-2007). NPDS reported an average of 173 exposure calls for ciguatoxin and 200 exposure calls for scombroid fish poisoning annually (2005-2009). After adjusting for undercounting, we estimated 15,910 (90% credible interval [CrI] 4140-37,408) ciguatera fish-poisoning illnesses annually, resulting in 343 (90% CrI 69-851) hospitalizations and three deaths (90% CrI 1-7). We estimated 35,142 (90% CrI: 10,496-78,128) scombroid fish-poisoning illnesses, resulting in 162 (90% CrI 0-558) hospitalizations and 0 deaths. Ciguatera and scombroid fish poisonings affect more Americans than reported in surveillance systems. Although additional data can improve these assessments, the estimated number of illnesses caused by seafood intoxication illuminates this public health problem. Efforts, including education, can reduce ciguatera and scombroid fish poisonings.

Effects of environmental chemicals on fish thyroid function: Implications for fisheries and aquaculture in Australia.

PubMed

Nugegoda, Dayanthi; Kibria, Golam

2017-04-01

Numerous environmental stressors exert acute or chronic effects on the fish thyroid cascade. Such effects could be mediated via thyroidal alterations, imbalance of plasma T4 and T3 levels or damage to the structure of the thyroidal tissues (thyroid hypertrophy, hyperplasia). The thyroidal system is intricately linked to other endocrine systems in vertebrates including the control of reproduction. Disruption of fish thyroid function by environmental stressors has the potential to result in deleterious effects including the inhibition of sperm production, reduction in egg production, gonad development, ovarian growth, swimming activity, fertilisation and increase in larval mortality. Thyroid hormones play a major role in the development and growth of fish, particularly during their early life stages, thus, thyroid disruption by environmental stressors could inhibit the growth of fish larvae and juveniles in wild fish and cultured species, limit fish seed production and result in a decline in wild fisheries. This review highlights the effects of several environmental toxicants including PBDE, PCBs, PCDD and PCDF, PAH/oil, phthalates, metals, pesticides, mixed pollutants/chemicals, cyanide; and other stressors including acid (low pH) and ammonia, on fish thyroid function. Environmental sources of chemical stressors and appropriate water quality guidelines to protect the freshwater and marine species for the relevant pollutants are also discussed including (when available) the Australian guidelines (2000) and Canadian water quality guidelines (where Australian guidelines are not available). To date there has been no published research on the effects of anthropogenic environmental pollutants on the thyroid system of any native Australian fish species. However, the detection of high risk chemicals (notably PBDEs, PCBs, PAHs, metals and pesticides) in Australian waterways and Australian fish and shellfish implies that thyroid disruption of Australian wild fish and aquacultured species could occur. It is therefore imperative that the effects of such pollutants on the thyroid system of Australian native fish be investigated. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular biology and physiology of the melanocortin system in fish: a review.

PubMed

Metz, Juriaan R; Peters, Joris J M; Flik, Gert

2006-09-01

The melanocortin system consists of melanocortin peptides derived from the proopiomelanocortin gene (in particular adrenocorticotropic hormone, ACTH, and melanocyte-stimulating hormones, MSH) and five melanocortin receptor subtypes (MC1R-MC5R). Knowledge of the melanocortin system in fish is still limited, but information on the receptor part of the system is very rapidly growing. The melanocortin receptors (MCRs) have been recently cloned from several species of fish. The amino acid sequences appear remarkably well conserved. Pharmacological characterisation studies of the first identified piscine MCRs indicate that ACTH may be the original ligand for the MCRs, while the MSH peptides gained specialised functions in the course of evolution. Considering the tissue distribution of the MCRs, there are two distinctions between mammals and fish: where in mammals the MC4R is exclusively expressed in the central nervous system, in the fish species examined so far it is also peripherally expressed. It does however, alike the situation in mammals, likely play a key role in the central regulation of food intake and energy balance. Not only the MCRs, but also many other factors involved herewith, have been found in fish and roughly appear to function similarly as in mammals. The second difference is the distribution of the MC5R, which appears less widely expressed in fish than in mammals. Considering the available data it is predicted that, in mammals and fish alike, skin colouration is mediated via MC1R and steroidogenesis via MC2R. This review provides a short overview of the basic molecular characteristics, pharmacology, and tissue distribution of the MCRs in the fish investigated up to now, as well as their physiological role in the processes of skin colouration, steroidogenesis, and feeding behaviour.

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.

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

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.

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).

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

Multiple cues produced by a robotic fish modulate aggressive behaviour in Siamese fighting fishes.

PubMed

Romano, Donato; Benelli, Giovanni; Donati, Elisa; Remorini, Damiano; Canale, Angelo; Stefanini, Cesare

2017-07-05

The use of robotics to establish social interactions between animals and robots, represents an elegant and innovative method to investigate animal behaviour. However, robots are still underused to investigate high complex and flexible behaviours, such as aggression. Here, Betta splendens was tested as model system to shed light on the effect of a robotic fish eliciting aggression. We evaluated how multiple signal systems, including a light stimulus, affect aggressive responses in B. splendens. Furthermore, we conducted experiments to estimate if aggressive responses were triggered by the biomimetic shape of fish replica, or whether any intruder object was effective as well. Male fishes showed longer and higher aggressive displays as puzzled stimuli from the fish replica increased. When the fish replica emitted its full sequence of cues, the intensity of aggression exceeded even that produced by real fish opponents. Fish replica shape was necessary for conspecific opponent perception, evoking significant aggressive responses. Overall, this study highlights that the efficacy of an artificial opponent eliciting aggressive behaviour in fish can be boosted by exposure to multiple signals. Optimizing the cue combination delivered by the robotic fish replica may be helpful to predict escalating levels of aggression.

Seasonality of parasitic helminths of Leporinus macrocephalus and their parasitism rates in farming systems in the Amazon.

PubMed

Martins, Williane Maria de Oliveira; Justo, Márcia Cristina Nascimento; Cárdenas, Melissa Querido; Cohen, Simone Chinicz

2017-01-01

The objective of the present study was to analyze the seasonality of parasitic helminths of Leporinus macrocephalus from fish farms in the municipality of Cruzeiro do Sul, Acre, Brazil, and their parasitism rates. Between June 2014 and March 2015, 200 specimens were sampled from two fish farms: one with a semi-intensive system and the other with an extensive system (100 fish from each farm: 50 during the dry season and 50 during the rainy season). Fifteen species of parasites were found, with seasonal variations of some according to the farming system. In the semi-intensive fish farm, there was greater prevalence of infection during the dry season. Also, Urocleidoides paradoxus, Procamallanus (Spirocamallanus) inopinatus, Goezia leporini and Rhabdochona (Rhabdochona) acuminata presented differences in their parasitism rates between the seasons. In the extensive fish farm, no variation in the prevalence of infection was observed between the seasons and two species Tereancistrum parvus and G. leporini demonstrated differences only regarding the mean intensity of infection. The data presented here may help fish farmers to understand the parasite dynamics of L. macrocephalus in farming systems during the dry and rainy seasons in the state of Acre.

Bioremediation using Gracilaria chouae co-cultured with Sparus macrocephalus to manage the nitrogen and phosphorous balance in an IMTA system in Xiangshan Bay, China.

PubMed

Wu, Hailong; Huo, Yuanzi; Han, Fang; Liu, Yuanyuan; He, Peimin

2015-02-15

A cage experiment using the red alga Gracilaria chouae co-cultured with the black seabream Sparus macrocephalus in Xiangshan Bay, China was conducted to measure the nutrient flux of the integrated multi-trophic aquaculture (IMTA) system. Results showed that trash fish were the main nutrient input contributor and adult fish were the main nutrient output contributor in the system. Contents of N and P in adult fish accounted for 54.45% and 59.48% of N and P in trash fish and fry, which suggests that 45.55% of N and 40.52% of P generated by fish farming were released into to the water. G. chouae proved to be an efficient bioremediation species in this IMTA system. To balance the excess nutrients generated by the system, 231.09 kg of seedlings should be cultured and 5315.07 kg of adult seaweed should be harvested. Copyright © 2014 Elsevier Ltd. All rights reserved.

Native fishes of arid lands: A dwindling resource of the desert southwest

Treesearch

John N. Rinne; W. L. Minckley

1991-01-01

Includes color photos of 44 species of fishes, many published for the first time. Text describes aquatic systems in the mountains and deserts of the Southwest, the unique fishes they support, and habitats the fishes need.

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. 

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.

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.

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

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.

Guiding out-migrating juvenile sea lamprey (Petromyzon marinus) with pulsed direct current

USGS Publications Warehouse

Johnson, Nicholas S.; Miehls, Scott M.

2014-01-01

Non-physical stimuli can deter or guide fish without affecting water flow or navigation and therefore have been investigated to improve fish passage at anthropogenic barriers and to control movement of invasive fish. Upstream fish migration can be blocked or guided without physical structure by electrifying the water, but directional downstream fish guidance with electricity has received little attention. We tested two non-uniform pulsed direct current electric systems, each having different electrode orientations (vertical versus horizontal), to determine their ability to guide out-migrating juvenile sea lamprey (Petromyzon marinus) and rainbow trout (Oncorhynchus mykiss). Both systems guided significantly more juvenile sea lamprey to a specific location in our experimental raceway when activated than when deactivated, but guidance efficiency decreased at the highest water velocities tested. At the electric field setting that effectively guided sea lamprey, rainbow trout were guided by the vertical electrode system, but most were blocked by the horizontal electrode system. Additional research should characterize the response of other species to non-uniform fields of pulsed DC and develop electrode configurations that guide fish over a range of water velocity.

Bioaccumulation and oxidative stress caused by pesticides in Cyprinus carpio reared in a rice-fish system.

PubMed

Clasen, Barbara; Loro, Vania L; Murussi, Camila R; Tiecher, Tadeu Luis; Moraes, Bibiana; Zanella, Renato

2018-06-01

Nowadays, many irrigated rice producers have adopted the rice-fish farming systems, in which fish are reared in the same environment as rice is grown. These animals can biologically control many pests that disturb the crop, as well as increase the income of producers when they are reared in the same area as rice. However, a large variety of pesticides is often used for pest control in conventional irrigated rice crops, and fish are exposed to different pesticide concentrations and active ingredients. Thus, the aim of the current study is to assess the potential risks of these pesticides to freshwater fish (Cyprinus carpio) cultured in integrated rice-fish farming systems. We assessed five pesticides widely used in rice culture. This is the first report on the bioaccumulation of the insecticides lambda-cyhalothrin + thiamethoxam and clorantraniliprole and of the fungicide tebuconazole + trifloxystrobin associated with oxidative stress and with enzymatic and non-enzymatic parameters in edible fish samples reared in integrated in rice-fish farming systems. After 100 days of exposure, lambda-cyhalothrin and tebuconazole bioaccumulated in carp muscles. Acethylcholinesterase activity in the brain was lower in the experimental group than in the control group. Overall, the biochemical analyses showed increased responses in the experimental groups in comparison to the controls. Lipid peroxidation levels increased in the liver, gills and muscles. Protein oxidation increased in the liver and muscles. Catalase activity increased in the liver, and glutathione S-transferase increased in the liver, gills and muscles. Results demonstrate that these pesticides have severe adverse consequences in fish and indicate their potential risk to human health due to their bioaccumulation in farmed fish. Copyright © 2018 Elsevier B.V. All rights reserved.

The Paraty artisanal fishery (southeastern Brazilian coast): ethnoecology and management of a social-ecological system (SES).

PubMed

Begossi, Alpina; Salyvonchyk, Svetlana; Nora, Vinicius; Lopes, Priscila F; Silvano, Renato A M

2012-06-27

This study intends to give recommendations to the management of Paraty fishery in Brazil through an interplay of local and scientific knowledge. In particular, the objectives are the following: 1) to describe the Paraty fishery; 2) to compare the fishermen's local ecological knowledge with recorded fish landings and previous studies in Paraty; 3) to combine the data on local fishing and on local/Caiçara livelihoods with the SES (social-ecological systems) Model. The methods include a systematic survey of fishing in Tarituba and Praia Grande, which are located in the northern end and the central part of the Paraty municipality, respectively. For four days each month, systematic data on catches at landing points were collected, as well as macroscopic gonad analysis data for the fishes Centropomus parallelus and C. undecimalis (snook, robalo), Epinephelus marginatus (grouper, garoupa), Scomberomorus cavalla (King mackerel, cavala), and Lutjanus synagris (Lane snapper, vermelho). Spring and summer are important seasons during which some species reproduce, and the integration of fishing periods for some target species could assist in fishing management through the use of closed seasons. Fishermen could obtain complementary earnings from tourism and from the "defeso system" (closed season including a salary payment) to conserve fishing stocks. The SES model facilitates an understanding of the historical context of fishing, its economic importance for local livelihoods, the constraints from conservation measures that affect fishermen, and the management processes that already exist, such as the defeso. If used to integrate fishing with complementary activities (tourism), such a system could improve the responsibility of fishermen regarding the conservation of fish stocks.

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.

Effects of Ocean Acidification on Fish Eggs and Larvae in Laboratory Experiments and Naturally High-pCO2 Upwelling Systems

NASA Astrophysics Data System (ADS)

Shen, S.; Checkley, D. M., Jr.

2016-02-01

We investigated the effects of elevated pCO2 on (1) the morphology and behavior of fish larvae in laboratory experiments and (2) the distribution and abundance of fish eggs and larvae in an upwelling system. The vestibulo-ocular reflex (VOR) is a compensatory eye rotation that stabilizes images during movement and is initiated by utricular otolith movement. It is critically important for survival. We identified a 38% increase in the area of the utricular otoliths of larval white seabass (Atractoscion nobilis) reared at 2500 μatm pCO2 (treatment) compared to that of larvae reared at 400 μatm pCO2 (control). Despite the increase in otolith size, the mean gain of treatment larvae (0.39 ± 0.05, n= 28) was not statistically different from that of control larvae (0.30 ± 0.03, n= 20). During a fisheries research cruise in the Peruvian upwelling system in 2013, we collected eggs and larvae of Peruvian anchoveta (Engraulis ringens) over a wide range of pCO2, from 200-1200 μatm. Anchoveta support the world's largest single-species fishery and reside in arguably the most persistently high-pCO2 environment in the ocean. The probability of egg capture was maximal at the lowest (<350 μatm) as well as highest (>1000 μatm) pCO2 and increased with increasing chlorophyll a concentration. Larval abundance was maximal in the mid-range of zooplankton biovolume (1-3 cm3/1,000 m3). The occurrence of eggs in high pCO2 and relationship of eggs and larvae to food availability are consistent with the hypothesis that anchoveta tolerate a high pCO2 and food environment. Our research on the early life stages of these two fish leads us to believe that species that have evolved in high-pCO2 environments (e.g., anchoveta) may be able to cope with OA. Furthermore, OA may have only subtle effects on behaviors that are critical for survival (e.g., VOR).

The use of vertical constructed wetland and ultrasound in aquaponic systems.

PubMed

Krivograd Klemenčič, A; Griessler Bulc, T

2015-01-01

Treatment performance, fish production, crop plant biomass production, water consumption, and water use efficiency of a pilot aquaponic system for small-scale land-based cyprinid fish farms were evaluated. The system consisted of a 36 m(3) Pond A with an initial carp load of 0.6 kg/m(3); of a treatment chain with a lamellar settler, a roughing filter, a vertical constructed wetland filled with expanded clay and planted with tomatoes; and of a low power ultrasound unit installed in the corner of the pond. The average circulation of the water in the system was 1.2 times per day. Pond A was compared with Pond B of the same dimensions and fish load but with no treatment chain or ultrasound. The treatment chain was efficient in mass removal of total suspended solids , biochemical oxygen demand, chemical oxygen demand, NH4-N, total nitrogen, and total phosphorous (57, 49, 35, 42, 31, and 25 %, respectively). Negative removal of NO3-N, NO2-N, and PO4-P indicated the need for the introduction of additional hydroponic beds in the system. Pond A had markedly lower nutrient concentrations compared with Pond B. Fish body weight increase and specific growth rate in Pond A were higher than in Pond B (102.6 %, 72.1 %; 0.19 %/day, 0.14 %/day, respectively) indicating better rearing conditions in Pond A. Tomato biomass production was high. Water use efficiency was higher in Pond A compared with Pond B (0.31 kg of produced fish/m(3) inflow water and 0.22 kg of produced fish/m(3) inflow water, respectively). The presented aquaponic system could be useful for semi-natural fish farming with fish loads up to 2 kg/m(3).

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.

Fish welfare assurance system: initial steps to set up an effective tool to safeguard and monitor farmed fish welfare at a company level.

PubMed

van de Vis, J W; Poelman, M; Lambooij, E; Bégout, M-L; Pilarczyk, M

2012-02-01

The objective was to take a first step in the development of a process-oriented quality assurance (QA) system for monitoring and safeguarding of fish welfare at a company level. A process-oriented approach is focused on preventing hazards and involves establishment of critical steps in a process that requires careful control. The seven principles of the Hazard Analysis Critical Control Points (HACCP) concept were used as a framework to establish the QA system. HACCP is an internationally agreed approach for management of food safety, which was adapted for the purpose of safeguarding and monitoring the welfare of farmed fish. As the main focus of this QA system is farmed fish welfare assurance at a company level, it was named Fish Welfare Assurance System (FWAS). In this paper we present the initial steps of setting up FWAS for on growing of sea bass (Dicentrarchus labrax), carp (Cyprinus carpio) and European eel (Anguilla anguilla). Four major hazards were selected, which were fish species dependent. Critical Control Points (CCPs) that need to be controlled to minimize or avoid the four hazards are presented. For FWAS, monitoring of CCPs at a farm level is essential. For monitoring purposes, Operational Welfare Indicators (OWIs) are needed to establish whether critical biotic, abiotic, managerial and environmental factors are controlled. For the OWIs we present critical limits/target values. A critical limit is the maximum or minimum value to which a factor must be controlled at a critical control point to prevent, eliminate or reduce a hazard to an acceptable level. For managerial factors target levels are more appropriate than critical limits. Regarding the international trade of farmed fish products, we propose that FWAS needs to be standardized in aquaculture chains. For this standardization a consensus on the concept of fish welfare, methods to assess welfare objectively and knowledge on the needs of farmed fish are required.

New approach for monitoring fish stress: A novel enzyme-functionalized label-free immunosensor system for detecting cortisol levels in fish.

PubMed

Wu, Haiyun; Ohnuki, Hitoshi; Ota, Shirei; Murata, Masataka; Yoshiura, Yasutoshi; Endo, Hideaki

2017-07-15

Fishes display a wide variation in their physiological responses to stress, which is clearly evident in the plasma corticosteroid changes, chiefly cortisol levels in fish. As a well-known indicator of fish stress, a simple and rapid method for detecting cortisol changes especially sudden increases is desired. In this study, we describe an enzyme-functionalized label-free immunosensor system for detecting fish cortisol levels. Detection of cortisol using amperometry was achieved by immobilizing both anti-cortisol antibody (selective detection of cortisol) and glucose oxidase (signal amplification and non-toxic measurement) on an Au electrode surface with a self-assembled monolayer. This system is based on the maximum glucose oxidation output current change induced by the generation of a non-conductive antigen-antibody complex, which depends on the levels of cortisol in the sample. The immunosensor responded to cortisol levels with a linear decrease in the current in the range of 1.25-200ngml -1 (R=0.964). Since the dynamic range of the sensor can cover the normal range of plasma cortisol in fish, the samples obtained from the fish did not need to be diluted. Further, electrochemical measurement of one sample required only ~30min. The sensor system was applied to determine the cortisol levels in plasma sampled from Nile tilapia (Oreochromis niloticus), which were then compared with levels of the same samples determined using the conventional method (ELISA). Values determined using both methods were well correlated. These findings suggest that the proposed label-free immunosensor could be useful for rapid and convenient analysis of cortisol levels in fish without sample dilution. We also believe that the proposed system could be integrated in a miniaturized potentiostat for point-of-care cortisol detection and useful as a portable diagnostic in fish farms in the future. Copyright © 2016 Elsevier B.V. All rights reserved.

Neuronal Organization of Deep Brain Opsin Photoreceptors in Adult Teleosts

PubMed Central

Hang, Chong Yee; Kitahashi, Takashi; Parhar, Ishwar S.

2016-01-01

Biological impacts of light beyond vision, i.e., non-visual functions of light, signify the need to better understand light detection (or photoreception) systems in vertebrates. Photopigments, which comprise light-absorbing chromophores bound to a variety of G-protein coupled receptor opsins, are responsible for visual and non-visual photoreception. Non-visual opsin photopigments in the retina of mammals and extra-retinal tissues of non-mammals play an important role in non-image-forming functions of light, e.g., biological rhythms and seasonal reproduction. This review highlights the role of opsin photoreceptors in the deep brain, which could involve conserved neurochemical systems that control different time- and light-dependent physiologies in in non-mammalian vertebrates including teleost fish. PMID:27199680

Asian fish tapeworm Bothriocephalus acheilognathi in the desert southwestern United States.

PubMed

Archdeacon, Thomas P; Iles, Alison; Kline, S Jason; Bonar, Scott A

2010-12-01

The Asian fish tapeworm Bothriocephalus acheilognathi (Cestoda: Bothriocephalidea) is an introduced fish parasite in the southwestern United States and is often considered a serious threat to native desert fishes. Determining the geographic distribution of nonnative fish parasites is important for recovery efforts of native fishes. We examined 1,140 individuals belonging to nine fish species from southwestern U.S. streams and springs between January 2005 and April 2007. The Asian fish tapeworm was present in the Gila River, Salt River, Verde River, San Pedro River, Aravaipa Creek, and Fossil Creek, Arizona, and in Lake Tuendae at Zzyzx Springs and Afton Canyon of the Mojave River, California. Overall prevalence of the Asian fish tapeworm in Arizona fish populations was 19% (range = 0-100%) and varied by location, time, and fish species. In California, the prevalence, abundance, and intensity of the Asian fish tapeworm in Mohave tui chub Gila bicolor mohavensis were higher during warmer months than during cooler months. Three new definitive host species--Yaqui chub G. purpurea, headwater chub G. nigra, and longfin dace agosia chrysogaster--were identified. Widespread occurrence of the Asian fish tapeworm in southwestern U.S. waters suggests that the lack of detection in other systems where nonnative fishes occur is due to a lack of effort as opposed to true absence of the parasite. To limit further spread of diseases to small, isolated systems, we recommend treatment for both endo- and exoparasites when management actions include translocation of fishes.

Identifying across‐system sources of variation in a generalist freshwater fish: Correlates of total and size‐specific abundance of yellow perch

USGS Publications Warehouse

Carey, Michael P.; Mather, M. E.

2009-01-01

Variation in fish abundance across systems presents a challenge to our understanding of fish populations because it limits our ability to predict and transfer basic ecological principles to applied problems. Yellow perch (Perca flavescens) is an ideal species for exploring environmental and biotic correlates across system because it is widely distributed and physiologically tolerant. In 16 small, adjacent systems that span a wide range of environmental and biotic conditions, yellow perch were sampled with a standard suite of gear. Water quality, morphometry, vegetation, invertebrates and fish communities were concurrently measured. Multimodel inference was used to prioritise regressors for the entire yellow perch sample and three size groups (35-80, 81-180, ≥181 mm TL). Across systems, pH and fish richness were identified as the key drivers of yellow perch abundance. At very low pH (<4.0), few fish species and few yellow perch individuals were found. At ponds with moderately low pH (4.0–4.8), numbers of yellow perch increased. Ponds with high pH (>4.8) had many other species and few yellow perch. Similar patterns for pH and fish community were observed for the two largest‐size classes. Negative interactions were observed between the medium‐ and large‐sized yellow perch and between the largest and smallest yellow perch, although interspecific interactions were weaker than expected. This examination of variability for an indicator species and its component‐size classes provides ecological understanding that can help frame the larger‐scale sampling programs needed for the conservation of freshwater fish.

Trophic flows, ecosystem structure and fishing impacts in the South Catalan Sea, Northwestern Mediterranean

NASA Astrophysics Data System (ADS)

Coll, Marta; Palomera, Isabel; Tudela, Sergi; Sardà, Francesc

2006-01-01

An exploited ecosystem from the continental shelf and upper slope of the Northwestern Mediterranean Sea was described by means of an Ecopath mass-balance model with the aim of characterising its functioning and structure and describing the ecosystem impacts of fishing. This application included some complexities added to the general modelling methodology due to the high biodiversity of the Mediterranean Sea and the multispecific nature of the fishery, and to the difficulties of working with fishing data which are usually irregularly or imprecisely collected. The model comprised 40 functional groups including primary producers, the main species of benthic, demersal and pelagic invertebrates, fishes and non-fish vertebrates and three detritus groups. In addition, trawling, purse seine, longline and troll bait fishing fleets were included. Results showed that the functional groups were organized into four trophic levels with the highest levels corresponding to anglerfish, dolphins, large pelagic fishes and adult hake. The system was dominated by the pelagic fraction, where sardine and anchovy prevailed in terms of fish biomasses and catches. Detritus and detritivorous groups also played key roles in the ecosystem and important coupled pelagic-demersal interactions were described. Considering Odum's theory of ecosystem development, the ecosystem was placed on an intermediate-low developmental stage due, at least partially, to the impact of fishing activity. This highlighted the high intensity of fishing in the ecosystem, in accordance with the general assessment of western Mediterranean marine resources, and fishing fleets were ranked as top predators of the system. The low trophic level of the catch was in line with the long history of exploitation in the area. However, the steady decline of pelagic landings between 1994 and 2003, coupled with a decrease of the pelagic biomass within the system, underlined the low resistance of the system in front of perturbations. This decline was reproduced under Ecosim dynamic simulations combining different scenarios of moderate increase of fishing effort and an environmental forcing affecting the availability of preys to small and medium-sized pelagic fishes under wasp-waist flow control.

Natural flow regimes, nonnative fishes, and native fish persistence in arid-land river systems.

PubMed

Propst, David L; Gido, Keith B; Stefferud, Jerome A

2008-07-01

Escalating demands for water have led to substantial modifications of river systems in arid regions, which coupled with the widespread invasion of nonnative organisms, have increased the vulnerability of native aquatic species to extirpation. Whereas a number of studies have evaluated the role of modified flow regimes and nonnative species on native aquatic assemblages, few have been conducted where the compounding effects of modified flow regimes and established nonnatives do not confound interpretations, particularly at spatial and temporal scales that are relevant to conservation of species at a range-wide level. By evaluating a 19-year data set across six sites in the relatively unaltered upper Gila River basin, New Mexico, USA, we tested how natural flow regimes and presence of nonnative species affected long-term stability of native fish assemblages. Overall, we found that native fish density was greatest during a wet period at the beginning of our study and declined during a dry period near the end of the study. Nonnative fishes, particularly predators, generally responded in opposite directions to these climatic cycles. Our data suggested that chronic presence of nonnative fishes, coupled with naturally low flows reduced abundance of individual species and compromised persistence of native fish assemblages. We also found that a natural flow regime alone was unlikely to ensure persistence of native fish assemblages. Rather, active management that maintains natural flow regimes while concurrently suppressing or excluding nonnative fishes from remaining native fish strongholds is critical to conservation of native fish assemblages in a system, such as the upper Gila River drainage, with comparatively little anthropogenic modification.

Characterization of Atlantic cod spawning habitat and behavior in Icelandic coastal waters

USGS Publications Warehouse

Grabowski, Timothy B.; Boswell, Kevin M.; McAdam, Bruce J.; Wells, R. J. David; Marteinsdóttir, Gudrún

2012-01-01

The physical habitat used during spawning may potentially be an important factor affecting reproductive output of broadcast spawning marine fishes, particularly for species with complex, substrate-oriented mating systems and behaviors, such as Atlantic cod Gadus morhua. We characterized the habitat use and behavior of spawning Atlantic cod at two locations off the coast of southwestern Iceland during a 2-d research cruise (15–16 April 2009). We simultaneously operated two different active hydroacoustic gear types, a split beam echosounder and a dual frequency imaging sonar (DIDSON), as well as a remotely operated underwater vehicle (ROV). A total of five fish species were identified through ROV surveys: including cusk Brosme brosme, Atlantic cod, haddock Melanogrammus aeglefinus, lemon sole Microstomus kitt, and Atlantic redfish Sebastes spp. Of the three habitats identified in the acoustic surveys, the transitional habitat between boulder/lava field and sand habitats was characterized by greater fish density and acoustic target strength compared to that of sand or boulder/lava field habitats independently. Atlantic cod were observed behaving in a manner consistent with published descriptions of spawning. Individuals were observed ascending 1–5 m into the water column from the bottom at an average vertical swimming speed of 0.20–0.25 m s−1 and maintained an average spacing of 1.0–1.4 m between individuals. Our results suggest that cod do not choose spawning locations indiscriminately despite the fact that it is a broadcast spawning fish with planktonic eggs that are released well above the seafloor.

Characterization of Atlantic Cod Spawning Habitat and Behavior in Icelandic Coastal Waters

PubMed Central

Grabowski, Timothy B.; Boswell, Kevin M.; McAdam, Bruce J.; Wells, R. J. David; Marteinsdóttir, Guđrún

2012-01-01

The physical habitat used during spawning may potentially be an important factor affecting reproductive output of broadcast spawning marine fishes, particularly for species with complex, substrate-oriented mating systems and behaviors, such as Atlantic cod Gadus morhua. We characterized the habitat use and behavior of spawning Atlantic cod at two locations off the coast of southwestern Iceland during a 2-d research cruise (15–16 April 2009). We simultaneously operated two different active hydroacoustic gear types, a split beam echosounder and a dual frequency imaging sonar (DIDSON), as well as a remotely operated underwater vehicle (ROV). A total of five fish species were identified through ROV surveys: including cusk Brosme brosme, Atlantic cod, haddock Melanogrammus aeglefinus, lemon sole Microstomus kitt, and Atlantic redfish Sebastes spp. Of the three habitats identified in the acoustic surveys, the transitional habitat between boulder/lava field and sand habitats was characterized by greater fish density and acoustic target strength compared to that of sand or boulder/lava field habitats independently. Atlantic cod were observed behaving in a manner consistent with published descriptions of spawning. Individuals were observed ascending 1–5 m into the water column from the bottom at an average vertical swimming speed of 0.20–0.25 m s−1 and maintained an average spacing of 1.0–1.4 m between individuals. Our results suggest that cod do not choose spawning locations indiscriminately despite the fact that it is a broadcast spawning fish with planktonic eggs that are released well above the seafloor. PMID:23236471

Novel Fish Oil-based Bigel System for Controlled Drug Delivery and its Influence on Immunomodulatory Activity of Imiquimod Against Skin Cancer.

PubMed

Rehman, Khurram; Zulfakar, Mohd Hanif

2017-01-01

To characterize bigel system as a topical drug delivery vehicle and to establish the immunomodulatory role of imiquimod-fish oil combination against skin cancer and inflammation resulting from chemical carcinogenesis. Imiquimod-loaded fish oil bigel colloidal system was prepared using a blend of carbopol hydrogel and fish oil oleogel. Bigels were first characterized for their mechanical properties and compared to conventional gel systems. Ex vivo permeation studies were performed on murine skin to analyze the ability of the bigels to transport drug across skin and to predict the release mechanism via mathematical modelling. Furthermore, to analyze pharmacological effectiveness in skin cancer and controlling imiquimod-induced inflammatory side effects, imiquimod-fish oil combination was tested in vitro on epidermoid carcinoma cells and in vivo in Swiss albino mice cancer model. Imiquimod-loaded fish oil bigels exhibited higher drug availability inside the skin as compared to individual imiquimod hydrogel and oleogel controls through quasi-Fickian diffusion mechanism. Imiquimod-fish oil combination in bigel enhanced the antitumor effects and significantly reduced serum pro-inflammatory cytokine levels such as tumor necrosis factor-alpha and interleukin-6, and reducing tumor progression via inhibition of vascular endothelial growth factor. Imiquimod-fish oil combination also resulted in increased expression of interleukin-10, an anti-inflammatory cytokine, which could also aid anti-tumor activity against skin cancer. Imiquimod administration through a bigel vehicle along with fish oil could be beneficial for controlling imiquimod-induced inflammatory side effects and in the treatment of skin cancer.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

PubMed Central

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. Availability The database is available for free at http://mail.nbfgr.res.in/fbis/ PMID:22715304

Cost effective system for monitoring of fish migration with a camera

NASA Astrophysics Data System (ADS)

Sečnik, Matej; Brilly, Mitja; Vidmar, Andrej

2016-04-01

Within the European LIFE project Ljubljanica connects (LIFE10 NAT/SI/000142) we have developed a cost-effective solution for the monitoring of fish migration through the fish passes with the underwater camera. In the fish pass at Ambrožev trg and in the fish pass near the Fužine castle we installed a video camera called "Fishcam" to be able to monitor the migration of fish through the fish passes and success of its reconstruction. Live stream from fishcams installed in the fishpassesis available on our project website (http://ksh.fgg.uni-lj.si/ljubljanicaconnects/ang/12_camera). The system for the fish monitoring is made from two parts. First is the waterproof box for the computer with charger and the second part is the camera itself. We used a high sensitive Sony analogue camera. The advantage of this camera is that it has very good sensitivity in low light conditions, so it can take good quality pictures even at night with a minimum additional lighting. For the night recording we use additional IR reflector to illuminate passing fishes. The camera is connected to an 8-inch tablet PC. We decided to use a tablet PC because it is quite small, cheap, it is relatively fast and has a low power consumption. On the computer we use software which has advanced motion detection capabilities, so we can also detect the small fishes. When the fish is detected by a software, its photograph is automatically saved to local hard drive and for backup also on Google drive. The system for monitoring of fish migration has turned out to work very well. From the beginning of monitoring in June 2015 to end of the year there were more than 100.000 photographs produced. The first analysis of them was already prepared estimating fish species and their frequency in passing the fish pass.

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.

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.

2012-03-01

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. Up to the present, the extremely high data rate hampers water column backscatter investigations and more sophisticated visualization and processing techniques are needed. Here, we present water column backscatter data acquired with a 50 kHz prototype multibeam system over a period of 75 seconds. Display types are of swath-images as well as of a "re-sorted" singlebeam presentation. Thus, individual and/or groups of gas bubbles rising from the 24 m deep seafloor clearly emerge in the acoustic images, making it possible to estimate rise velocities. A sophisticated processing scheme is introduced to identify those rising gas bubbles in the hydroacoustic data. We apply a cross-correlation technique adapted from particle imaging velocimetry (PIV) to the acoustic backscatter images. Temporal and spatial drift patterns of the bubbles are assessed and are shown to match very well to measured and theoretical rise patterns. The application of this processing to our field data gives clear results with respect to unambiguous bubble detection and remote bubble rise velocimetry. The method can identify and exclude the main source of misinterpretations, i.e. fish-mediated echoes. Although image-based cross-correlation techniques are well known in the field of fluid mechanics for high resolution and non-inversive current flow field analysis, we present the first application of this technique as an acoustic bubble detector.

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.

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

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

Using Sound to Modify Fish Behavior at Power-Production and Water-Control Facilities: A Workshop December 12-13, 1995. Phase II: Final Report.

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

Carlson, Thomas J.; Popper, Arthur N.

1997-06-01

A workshop on ``Use of Sound for Fish Protection at Power-Production and Water-Control Facilities`` was held in Portland, Oregon on December 12--13, 1995. This workshop convened a 22-member panel of international experts from universities, industry, and government to share knowledge, questions, and ideas about using sound for fish guidance. Discussions involved in a broad range of indigenous migratory and resident fish species and fish-protection issues in river systems, with particular focus on the Columbia River Basin. Because the use of sound behavioral barriers for fish is very much in its infancy, the workshop was designed to address the many questionsmore » being asked by fishery managers and researchers about the feasibility and potential benefits of using sound to augment physical barriers for fish protection in the Columbia River system.« less

Growth and fillet quality attributes of five genetic strains of rainbow trout (Oncorhynchus mykiss) reared in a partial water reuse system and harvested at different sizes

USDA-ARS?s Scientific Manuscript database

Genetics and environment can interact to influence fish growth performance and product quality attributes. Interaction in recirculating aquaculture systems (RAS) makes selection of fish strain and harvest sizes critical for optimizing fish quality. Definition of growth performance and quality outcom...

Effects of cold-water corals on fish diversity and density (European continental margin: Arctic, NE Atlantic and Mediterranean Sea): Data from three baited lander systems

NASA Astrophysics Data System (ADS)

Linley, T. D.; Lavaleye, M.; Maiorano, P.; Bergman, M.; Capezzuto, F.; Cousins, N. J.; D'Onghia, G.; Duineveld, G.; Shields, M. A.; Sion, L.; Tursi, A.; Priede, I. G.

2017-11-01

Autonomous photographic landers are a low-impact survey method for the assessment of mobile fauna in situations where methods such as trawling are not feasible or ethical. Three institutions collaborated through the CoralFISH project, each using differing lander systems, to assess the effects of cold-water corals on fish diversity and density. The Biogenic Reef Ichthyofauna Lander (BRIL, Oceanlab), Autonomous Lander for Biological Experiments (ALBEX, NIOZ) and the Marine Environment MOnitoring system (MEMO, CoNISMa) were deployed in four CoralFISH European study regions covering the Arctic, NE Atlantic and Mediterranean, namely Northern Norway (275-310 m depth), Belgica Mound Province (686-1025 m depth), the Bay of Biscay (623-936 m depth), and Santa Maria di Leuca (547-670 m depth). A total of 33 deployments were carried out in the different regions. Both the time of first arrival (Tarr) and the maximum observed number of fish (MaxN) were standardised between the different lander systems and compared between coral and reference stations as indicators of local fish density. Fish reached significantly higher MaxN at the coral stations than at the reference stations. Fish were also found to have significantly lower Tarr in the coral areas in data obtained from the BRIL and MEMO landers. All data indicated that fish abundance is higher within the coral areas. Fish species diversity was higher within the coral areas of Atlantic Ocean while in Northern Norway and Santa Maria di Leuca coral areas, diversity was similar at coral and reference stations but a single dominant species (Brosme brosme and Conger conger respectively) showed much higher density within the coral areas. Indicating that, while cold-water coral reefs have a positive effect on fish diversity and/or abundance, this effect varies across Europe's reefs.

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.

Effects of experimental otter trawling on benthic assemblages on Western Bank, northwest Atlantic Ocean

NASA Astrophysics Data System (ADS)

Kenchington, Ellen L. R.; Gilkinson, Kent D.; MacIsaac, Kevin G.; Bourbonnais-Boyce, Cynthia; Kenchington, Trevor J.; Smith, Stephen J.; Gordon, Donald C., Jr.

2006-10-01

The effects of otter trawling on a hard-bottom ecosystem on Western Bank on Canada's Scotian Shelf were examined experimentally from 1997 to 1999 with an asymmetrical BACI design. The site was located within an area that had been closed to fishing since 1987 to protect juvenile haddock. An experimental line was trawled 12-14 times on three separate occasions over a 20 month period. The benthic macrofauna and megafauna were sampled before and after trawling on both impact and control lines with both a grab and a photographic system. The 100 grab samples collected contained 341 taxa, primarily polychaetes, amphipods and molluscs, the majority (60%) of which were epifaunal. Biomass was dominated by the horse-mussel Modiolus modiolus, a long-lived bivalve, while the tube-building amphipod Ericthonius fasciatus was the most abundant species. Through the study period the benthos on the control lines showed little qualitative or quantitative change in individual taxa or community metrics. However, the abundance of 24 individual taxa (polychaetes, amphipods, echinoderms and molluscs) changed significantly, with the majority of these increasing. This resulted in a significantly different relative abundance of taxa between years as detected through ANOSIM. A significant change in relative biomass amongst the taxa was also observed. Trawling had few detectable immediate effects on the abundance or biomass of individual taxa and none on community composition. A few taxa, primarily a mixture of polychaetes and amphipods, decreased significantly after trawling and data from fish stomachs collected during the experiment (Kenchington, E.L., Gordon Jr., D.C., Bourbonnais-Boyce, C., MacIsaac, K.G., Gilkinson, K.D., McKeown, D.L., Vass, W.P., 2005. Effects of experimental otter trawling on the feeding of demersal fish on Western Bank, Nova Scotia. Amer. Fish. Soc. Symp. 41, 391-409) showed that some of these were scavenged by demersal fish. Fifteen taxa showed significant decreases after trawling when the cumulative effects of trawling were considered. As in the analyses of individual years the species affected were primarily high turn-over species such as polychaetes and amphipods. Dominance curves prepared for both control and impact samples before trawling in 1997 and after trawling in 1999 showed a marked decrease in the biomass values of the highest ranking taxa, particularly of the first species, M. modiolus, only on the impact line at the conclusion of the experiment. The proportion of epifaunal biomass also declined significantly from 90% to 77% on the impact line by the conclusion of the experiment. These changes are in part due to trawl-induced damage and subsequent predation by demersal fish of the top ranking species. Analysis of the photographic images showed that the three top-ranking species in terms of biomass, M. modiolus, the tube-building polychaete Thelepus cincinnatus, and the brachiopod Terebratulina septentrionalis, were visibly damaged more than other species by the trawl gear. Two of these species, M. modiolus and T. cincinnatus, were preyed upon by scavenging demersal fish. The use of multiple sampling devices at the experimental site (grab, photographic system reported here and trawl and fish stomachs reported by Kenchington, E.L., Gordon Jr., D.C., Bourbonnais-Boyce, C., MacIsaac, K.G., Gilkinson, K.D., McKeown, D.L., Vass, W.P., 2005. Effects of experimental otter trawling on the feeding of demersal fish on Western Bank, Nova Scotia. Amer. Fish. Soc. Symp. 41, 391-409) enabled us to link trawl-induced changes to the benthos to predation by demersal fish.

Developing methods based on light sheet fluorescence microscopy for biophysical investigations of larval zebrafish

NASA Astrophysics Data System (ADS)

Taormina, Michael J.

Adapting the tools of optical microscopy to the large-scale dynamic systems encountered in the development of multicellular organisms provides a path toward understanding the physical processes necessary for complex life to form and function. Obtaining quantitatively meaningful results from such systems has been challenging due to difficulty spanning the spatial and temporal scales representative of the whole, while also observing the many individual members from which complex and collective behavior emerges. A three-dimensional imaging technique known as light sheet fluorescence microscopy provides a number of significant benefits for surmounting these challenges and studying developmental systems. A thin plane of fluorescence excitation light is produced such that it coincides with the focal plane of an imaging system, providing rapid acquisition of optically sectioned images that can be used to construct a three-dimensional rendition of a sample. I discuss the implementation of this technique for use in larva of the model vertebrate Danio rerio (zebrafish). The nature of light sheet imaging makes it especially well suited to the study of large systems while maintaining good spatial resolution and minimizing damage to the specimen from excessive exposure to excitation light. I show the results from a comparative study that demonstrates the ability to image certain developmental processes non-destructively, while in contrast confocal microscopy results in abnormal growth due to phototoxicity. I develop the application of light sheet microscopy to the study of a previously inaccessible system: the bacterial colonization of a host organism. Using the technique, we are able to obtain a survey of the intestinal tract of a larval zebrafish and observe the location of microbes as they grow and establish a stable population in an initially germ free fish. Finally, I describe a new technique to measure the fluid viscosity of this intestinal environment in vivo using magnetically driven particles. By imaging such particles as they are oscillated in a frequency chirped field, it is possible to calculate properties such as the viscosity of the material in which they are embedded. Here I provide the first known measurement of intestinal mucus rheology in vivo.

Establishment of a fish community in the hayden-rhodes and salt-gila aqueducts, Arizona

USGS Publications Warehouse

Mueller, G.

1996-01-01

Fish populations were studied in the Central Arizona Project's canal system during the first 4 years of aqueduct operation (1986-1989). Ichthyoplankton entering the canal from Lake Havasu averaged 1 larva/m3 during April-June 1987 and 1988. Larval fish densities increased significantly in downstream samples, substantiating diver observations that fish were spawning in the canal system. Of the 16 fish species collected, 14 were assumed to have originated from Lake Havasu and 2 were introduced by anglers from their bait buckets. Initially, the fish community was dominated numerically by threadfin shad Dorosoma petenense (>88%), centrarchids (< 10%), cyprinids (<2%), and striped bass Morone saxatilis (<1%). However, as annual water diversions increased from 13 x 108 m3 in 1986 to 9.4 x 108 m3 in 1989, community composition shifted from clupeids to centrarchids (70%). Fish densities dropped from an estimated 1,260 fish/ha in 1986 to 17 fish/ha in 1989, and biomass dropped from 116 to 73 kg/ha. Declines were attributed to higher operational velocities, associated scour, deprivation, and predation. Although initial populations adjusted downward to planned operational conditions, the fish community continued to represent a potentially valuable, but as yet unused, resource.

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.

Experimental verification of an interpolation algorithm for improved estimates of animal position

NASA Astrophysics Data System (ADS)

Schell, Chad; Jaffe, Jules S.

2004-07-01

This article presents experimental verification of an interpolation algorithm that was previously proposed in Jaffe [J. Acoust. Soc. Am. 105, 3168-3175 (1999)]. The goal of the algorithm is to improve estimates of both target position and target strength by minimizing a least-squares residual between noise-corrupted target measurement data and the output of a model of the sonar's amplitude response to a target at a set of known locations. Although this positional estimator was shown to be a maximum likelihood estimator, in principle, experimental verification was desired because of interest in understanding its true performance. Here, the accuracy of the algorithm is investigated by analyzing the correspondence between a target's true position and the algorithm's estimate. True target position was measured by precise translation of a small test target (bead) or from the analysis of images of fish from a coregistered optical imaging system. Results with the stationary spherical test bead in a high signal-to-noise environment indicate that a large increase in resolution is possible, while results with commercial aquarium fish indicate a smaller increase is obtainable. However, in both experiments the algorithm provides improved estimates of target position over those obtained by simply accepting the angular positions of the sonar beam with maximum output as target position. In addition, increased accuracy in target strength estimation is possible by considering the effects of the sonar beam patterns relative to the interpolated position. A benefit of the algorithm is that it can be applied ``ex post facto'' to existing data sets from commercial multibeam sonar systems when only the beam intensities have been stored after suitable calibration.

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.

Climate change effects on North American inland fish populations and assemblages

USGS Publications Warehouse

Lynch, Abigail J.; Myers, Bonnie; Chu, Cindy; Eby, Lisa A.; Falke, Jeffrey A.; Kovach, Ryan P.; Krabbenhoft, Trevor J.; Kwak, Thomas J.; Lyons, John; Paukert, Craig P.; Whitney, James E.

2016-01-01

Climate is a critical driver of many fish populations, assemblages, and aquatic communities. However, direct observational studies of climate change impacts on North American inland fishes are rare. In this synthesis, we (1) summarize climate trends that may influence North American inland fish populations and assemblages, (2) compile 31 peer-reviewed studies of documented climate change effects on North American inland fish populations and assemblages, and (3) highlight four case studies representing a variety of observed responses ranging from warmwater systems in the southwestern and southeastern United States to coldwater systems along the Pacific Coast and Canadian Shield. We conclude by identifying key data gaps and research needs to inform adaptive, ecosystem-based approaches to managing North American inland fishes and fisheries in a changing climate.

Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach

EPA Science Inventory

Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...

Closed-loop control of zebrafish response using a bioinspired robotic-fish in a preference test

PubMed Central

Kopman, Vladislav; Laut, Jeffrey; Polverino, Giovanni; Porfiri, Maurizio

2013-01-01

In this paper, we study the response of zebrafish to a robotic-fish whose morphology and colour pattern are inspired by zebrafish. Experiments are conducted in a three-chambered instrumented water tank where a robotic-fish is juxtaposed with an empty compartment, and the preference of live subjects is scored as the mean time spent in the vicinity of the tank's two lateral sides. The tail-beating of the robotic-fish is controlled in real-time based on feedback from fish motion to explore a spectrum of closed-loop systems, including proportional and integral controllers. Closed-loop control systems are complemented by open-loop strategies, wherein the tail-beat of the robotic-fish is independent of the fish motion. The preference space and the locomotory patterns of fish for each experimental condition are analysed and compared to understand the influence of real-time closed-loop control on zebrafish response. The results of this study show that zebrafish respond differently to the pattern of tail-beating motion executed by the robotic-fish. Specifically, the preference and behaviour of zebrafish depend on whether the robotic-fish tail-beating frequency is controlled as a function of fish motion and how such closed-loop control is implemented. PMID:23152102

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.).

PubMed

Ohmido, Nobuko; Iwata, Aiko; Kato, Seiji; Wako, Toshiyuki; Fukui, Kiichi

2018-01-01

A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver. 4.0 (CHIAS IV). Correlation between H3K9me2, an epigenetic marker and formation and/or maintenance of heterochromatin, thus was, clearly visualized. Then the pachytene chromosome map was unified with the existing somatic chromosome and linkage maps by physically mapping common DNA markers among them, such as a rice A genome specific tandem repeat sequence (TrsA), 5S and 45S ribosomal RNA genes, five bacterial artificial chromosome (BAC) clones, four P1 bacteriophage artificial chromosome (PAC) clones using multicolor fluorescence in situ hybridization (FISH). Detailed comparison between the locations of the DNA probes on the pachytene chromosomes using multicolor FISH, and the linkage map enabled determination of the chromosome number and short/long arms of individual pachytene chromosomes using the chromosome number and arm assignment designated for the linkage map. As a result, the quantitative pachytene chromosome map was unified with two other major rice chromosome maps representing somatic prometaphase chromosomes and genetic linkages. In conclusion, the unification of the three rice maps serves as an indispensable basic information, not only for an in-depth comparison between genetic and chromosomal data, but also for practical breeding programs.

Modelling Nitrogen Cycling in a Mariculture Ecosystem as a Tool to Evaluate its Outflow

NASA Astrophysics Data System (ADS)

Lefebvre, S.; Bacher, C.; Meuret, A.; Hussenot, J.

2001-03-01

A model was constructed to describe an intensive mariculture ecosystem growing sea bass ( Dicentrarchus labrax), located in the salt marshes of the Fiers d'Ars Bay on the French Atlantic coast, in order to assess nitrogen cycling within the system and nitrogen outflow from the system. The land-based system was separated into three main compartments: a seawater reservoir, fish ponds and a lagoon (sedimentation pond). Three submodels were built for simulation purposes: (1) a hydrological submodel which simulated water exchange; (2) a fish growth and excretion bioenergetic submodel; and (3) a nitrogen compound transformation and loss submodel (i.e. ammonification, nitrification and assimilation processes). A two-year sampling period of nitrogen water quality concentrations and fish growth was used to validate the model. The model fitted the observations of dissolved nitrogen components, fish growth and water fluxes on a daily basis in all the compartments. The dissolved inorganic nitrogen ranged widely and over time from 0·5 to 9 g N m -3within the system, depending on seawater supply and water temperature, without affecting fish growth. Fish feed was the most important input of nitrogen into the system. The mean average input of nitrogen in the feed was 205 kg N day -1, of which 19% was retained by fish, 4% accumulated in the sediment and 61% flowed from the system as dissolved components. The farm represented about 25% of the total dissolved nitrogen export from the bay, although the farm surface area was 100 times smaller than that of the bay.

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

Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates

PubMed Central

2013-01-01

Background Classical major histocompatibility complex (MHC) class II molecules play an essential role in presenting peptide antigens to CD4+ T lymphocytes in the acquired immune system. The non-classical class II DM molecule, HLA-DM in the case of humans, possesses critical function in assisting the classical MHC class II molecules for proper peptide loading and is highly conserved in tetrapod species. Although the absence of DM-like genes in teleost fish has been speculated based on the results of homology searches, it has not been definitively clear whether the DM system is truly specific for tetrapods or not. To obtain a clear answer, we comprehensively searched class II genes in representative teleost fish genomes and analyzed those genes regarding the critical functional features required for the DM system. Results We discovered a novel ancient class II group (DE) in teleost fish and classified teleost fish class II genes into three major groups (DA, DB and DE). Based on several criteria, we investigated the classical/non-classical nature of various class II genes and showed that only one of three groups (DA) exhibits classical-type characteristics. Analyses of predicted class II molecules revealed that the critical tryptophan residue required for a classical class II molecule in the DM system could be found only in some non-classical but not in classical-type class II molecules of teleost fish. Conclusions Teleost fish, a major group of vertebrates, do not possess the DM system for the classical class II peptide-loading and this sophisticated system has specially evolved in the tetrapod lineage. PMID:24279922

A Bioassay System Using Bioelectric Signals from Small Fish

NASA Astrophysics Data System (ADS)

Terawaki, Mitsuru; Soh, Zu; Hirano, Akira; Tsuji, Toshio

Although the quality of tap water is generally examined using chemical assay, this method cannot be used for examination in real time. Against such a background, the technique of fish bioassay has attracted attention as an approach that enables constant monitoring of aquatic contamination. The respiratory rhythms of fish are considered an efficient indicator for the ongoing assessment of water quality, since they are sensitive to chemicals and can be indirectly measured from bioelectric signals generated by breathing. In order to judge aquatic contamination accurately, it is necessary to measure bioelectric signals from fish swimming freely as well as to stably discriminate measured signals, which vary between individuals. However, no bioassay system meeting the above requirements has yet been established. This paper proposes a bioassay system using bioelectric signals generated from small fish in free-swimming conditions. The system records signals using multiple electrodes to cover the extensive measurement range required in a free-swimming environment, and automatically discriminates changes in water quality from signal frequency components. This discrimination is achieved through an ensemble classification method using probability neural networks to solve the problem of differences between individual fish. The paper also reports on the results of related validation experiments, which showed that the proposed system was able to stably discriminate between water conditions before and after bleach exposure.

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

50 CFR 32.4 - Opening of wildlife refuge areas to fishing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false Opening of wildlife refuge areas to fishing. 32.4 Section 32.4 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM HUNTING AND FISHING General Provisions...

50 CFR 32.4 - Opening of wildlife refuge areas to fishing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false Opening of wildlife refuge areas to fishing. 32.4 Section 32.4 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM HUNTING AND FISHING General Provisions...

50 CFR 32.4 - Opening of wildlife refuge areas to fishing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false Opening of wildlife refuge areas to fishing. 32.4 Section 32.4 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM HUNTING AND FISHING General Provisions...

50 CFR 32.4 - Opening of wildlife refuge areas to fishing.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false Opening of wildlife refuge areas to fishing. 32.4 Section 32.4 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM HUNTING AND FISHING General Provisions...

50 CFR 32.4 - Opening of wildlife refuge areas to fishing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Opening of wildlife refuge areas to fishing. 32.4 Section 32.4 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM HUNTING AND FISHING General Provisions...

36 CFR 13.470 - Subsistence fishing.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Subsistence fishing. 13.470 Section 13.470 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Subsistence § 13.470 Subsistence fishing. Fish may be taken by local...

36 CFR 13.470 - Subsistence fishing.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Subsistence fishing. 13.470 Section 13.470 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Subsistence § 13.470 Subsistence fishing. Fish may be taken by local...

36 CFR 13.470 - Subsistence fishing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Subsistence fishing. 13.470 Section 13.470 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Subsistence § 13.470 Subsistence fishing. Fish may be taken by local...

36 CFR 13.470 - Subsistence fishing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Subsistence fishing. 13.470 Section 13.470 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Subsistence § 13.470 Subsistence fishing. Fish may be taken by local...

36 CFR 13.470 - Subsistence fishing.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Subsistence fishing. 13.470 Section 13.470 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Subsistence § 13.470 Subsistence fishing. Fish may be taken by local...

Model study of St. Stephen powerhouse fish passage facilities, Cooper River rediversion project, South Carolina. Final report

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

Hite, J.E.; Murphy, T.E.

1998-09-01

This report documents a model study of the St. Stephen Power Plant, located in Berkely County, South Carolina. A previous model study revealed that the fish lift at the powerhouse could be improved by providing auxiliary attraction flows to the fish entrances. An auxiliary attraction flow (AAF) system was proposed that uses a siphon to obtain the auxiliary attraction water from the reservoir. The model investigations reported herein address the flow conditions at the discharge end of the siphon; the hydraulic aspects of the siphon are not addressed. Three different models were used to evaluate flow conditions at the dischargemore » end of the AAF system. A 1:25-scale model of the St. Stephen powerhouse was used to improve the fish entrance conditions and to evaluate the outlet conditions for the initial AAF system. As the investigations progressed, the design of the siphon discharge system was modified to include downstream fish migration and debris passage.« less

A multi-electrode biomimetic electrolocation sensor

NASA Astrophysics Data System (ADS)

Mayekar, K.; Damalla, D.; Gottwald, M.; Bousack, H.; von der Emde, G.

2012-04-01

We present the concept of an active multi-electrode catheter inspired by the electroreceptive system of the weakly electric fish, Gnathonemus petersii. The skin of this fish exhibits numerous electroreceptor organs which are capable of sensing a self induced electrical field. Our sensor is composed of a sending electrode and sixteen receiving electrodes. The electrical field produced by the sending electrode was measured by the receiving electrodes and objects were detected by the perturbation of the electrical field they induce. The intended application of such a sensor is in coronary diagnostics, in particular in distinguishing various types of plaques, which are major causes of heart attack. For calibration of the sensor system, finite element modeling (FEM) was performed. To validate the model, experimental measurements were carried out with two different systems. The physical system was glass tubing with metal and plastic wall insertions as targets. For the control of the experiment and for data acquisition, the software LabView designed for 17 electrodes was used. Different parameters of the electric images were analyzed for the prediction of the electrical properties and size of the inserted targets in the tube. Comparisons of the voltage modulations predicted from the FEM model and the experiments showed a good correspondence. It can be concluded that this novel biomimetic method can be further developed for detailed investigations of atherosclerotic lesions. Finally, we discuss various design strategies to optimize the output of the sensor using different simulated models to enhance target recognition.

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.

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

Biomass production and nitrogen dynamics in an integrated aquaculture/agriculture system

NASA Technical Reports Server (NTRS)

Owens, L. P.; Hall, C. R.

1990-01-01

A combined aquaculture/agriculture system that brings together the three major components of a Controlled Ecological Life Support System (CELSS) - biomass production, biomass processing, and waste recycling - was developed to evaluate ecological processes and hardware requirements necessary to assess the feasibility of and define design criteria for integration into the Kennedy Space Center (KSC) Breadboard Project. The system consists of a 1 square meter plant growth area, a 500 liter fish culture tank, and computerized monitoring and control hardware. Nutrients in the hydrophonic solution were derived from fish metabolites and fish food leachate. In five months of continuous operation, 27.0 kg of lettuce tops, 39.9 kg of roots and biofilm, and 6.6 kg of fish (wet weights) were produced with 12.7 kg of fish food input. Based on dry weights, a biomass conversion index of 0.52 was achieved. A nitrogen budget was derived to determine partitioning of nitrogen within various compartments of the system. Accumulating nitrogen in the hypoponic solution indicated a need to enlarge the plant growth area, potentially increasing the biomass production and improving the biomass conversion index.

Salmonella Weltevreden in integrated and non-integrated tilapia aquaculture systems in Guangdong, China.

PubMed

Li, Kang; Petersen, Gitte; Barco, Lisa; Hvidtfeldt, Kristian; Liu, Liping; Dalsgaard, Anders

2017-08-01

Integrated tilapia-pig farming, which uses manure from pigs as fertilizers in fish pond, is a traditional and common production system practised by small-scale farmers in South-east Asia. Although such systems may be environmentally sustainable, they also pose potential food safety hazards including transmission of faecal zoonotic pathogens and accumulation of antimicrobial and other chemical residues. This study aimed to determine differences in occurrence and characteristics of Salmonella spp. isolated from tilapia-pig and non-integrated aquaculture systems in Guangdong province, China. A total of 77 samples (9 pig feed, 19 fish feed, 9 pig faeces, 20 fish mucus and 20 fish intestine) from 10 tilapia-pig ponds and 10 non-integrated ponds were analysed. Salmonella spp. was found in fish mucus (20.0%), fish intestine (40.0%) and pig faeces (11.1%) from integrated ponds, and from fish mucus (40.0%) and fish intestine (40.0%) from non-integrated ponds. S. Weltevreden (76.5%) was by far the most common serovar showing limited antimicrobial resistance. One pig faeces sample contained S. Typhimurium whereas feed samples were found free of Salmonella spp.. DNA fingerprinting by the PFGE method showed a clonal relationship of S. Weltevreden which was supported by similar antimicrobial resistance patterns (sulfamethoxazole and trimethoprim resistance) as well as most isolates harbouring a 147-kb sized plasmid. The common finding of S. Weltevreden in both tilapia production systems indicates that this serovar may have a different ecology and increased survival in aquaculture environments in comparison with other Salmonella serovars. Further in vivo studies of the ecology of S. Weltevreden in aquaculture environments are needed. Copyright © 2017. Published by Elsevier Ltd.

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…

Dispersal and dam passage of sonic-tagged juvenile lake sturgeon in the upper Tennessee River

USGS Publications Warehouse

Collier, William R.; Bettoli, Phillip William; Scholten, George D.

2011-01-01

More than 90,000 state-endangered lake sturgeon (Acipenser fulvescens) have been stocked into the French Broad River, Holston River, and Fort Loudoun Lake in the upper Tennessee River system. Although incidental reports of anglers catching these fish have increased, little is known about their fate after stocking. Therefore, this study was conducted to evaluate lake sturgeon dispersal throughout the system. Seven submersible ultrasonic receivers were deployed in the upper Tennessee River system and 37 juvenile fish (mean fork length = 660 mm) were surgically implanted with ultrasonic transmitters in the fall of 2007. These fish were stocked at two sites in the headwaters of Fort Loudoun Lake. The receivers logged 1,345 detections of tagged fish and manual tracking located 32 of the 37 tagged lake sturgeon over 21 months. Ten (31%) tagged fish passed through Fort Loudoun Dam and were located downstream in the headwaters of Watts Bar Reservoir; the other tagged fish were still at large above Fort Loudoun Dam when tracking ceased in 2009. Of all fish stocked, three (9%) were last located in the French Broad River and none were located in the Holston River.

[Functional development of chemosensory systems in the ontogeny of fish].

PubMed

Kasumian, A O

2011-01-01

Regularities of the functional development of chemosensory systems in the ontogeny of fish has been studied, i.e., the olfactory system, the taste system, and the common chemical sense. The olfactory system begins to function and provides response of juveniles to chemical signals before the taste system. Embryos that have hatched from coating but that do not yet feed exhibit nonspecialized motor responses to olfactory stimuli already. Immediately after the transition to exogenous nutrition, olfactory sensitivity to signals which elicit defensive and feeding behavioral responses begins to form and the ability to differentiate between similar odors develops. The reception of a limited number of taste stimuli occurs in the larvae during the transition to exogenous nutrition. With age, the spectrum of effective taste substances expands and the time spent on the definition of palatability by juvenile fishes reduces. Functional development of individual components of the taste system arises heterochronously, i.e., the outer (extraoral) form of taste reception arises earlier and more rapidly, and the buccal (intraoral) form of taste reception arises slower. No information is available about the functional development of the common chemical sense in the ontogeny of fish. It is assumed that the function of the chemosensory system arises in fish in early larval instar.

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.

Autonomic innervation of the fish gut.

PubMed

Olsson, Catharina

2009-01-01

The enteric nervous system follows a similar overall arrangement in all vertebrate groups. In fish, the majority of nerve cell bodies are found in the myenteric plexus, innervating muscles, blood vessels and glands. In this review, I describe similarities and differences in size, shape and transmitter content in enteric neurons in different fish species and also in comparison with other vertebrates, foremost mammals. The use of different histological and immunochemical methods is reviewed in a historical perspective including advantages and disadvantages of different methods. Lately, zebrafish have become an important model species for developmental studies of the nervous system, including the enteric nervous system, and this is briefly discussed. Finally, examples of how the enteric nervous system controls gut activity in fish is presented, focussing on the effect on gastrointestinal motility.

Using a trichromatic CCD camera for spectral skylight estimation.

PubMed

López-Alvarez, Miguel A; Hernández-Andrés, Javier; Romero, Javier; Olmo, F J; Cazorla, A; Alados-Arboledas, L

2008-12-01

In a previous work [J. Opt. Soc. Am. A 24, 942-956 (2007)] we showed how to design an optimum multispectral system aimed at spectral recovery of skylight. Since high-resolution multispectral images of skylight could be interesting for many scientific disciplines, here we also propose a nonoptimum but much cheaper and faster approach to achieve this goal by using a trichromatic RGB charge-coupled device (CCD) digital camera. The camera is attached to a fish-eye lens, hence permitting us to obtain a spectrum of every point of the skydome corresponding to each pixel of the image. In this work we show how to apply multispectral techniques to the sensors' responses of a common trichromatic camera in order to obtain skylight spectra from them. This spectral information is accurate enough to estimate experimental values of some climate parameters or to be used in algorithms for automatic cloud detection, among many other possible scientific applications.

Two-photon calcium imaging during fictive navigation in virtual environments

PubMed Central

Ahrens, Misha B.; Huang, Kuo Hua; Narayan, Sujatha; Mensh, Brett D.; Engert, Florian

2013-01-01

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features—such as turning responses to whole-field motion and dark avoidance—are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior. PMID:23761738

Two-photon calcium imaging during fictive navigation in virtual environments.

PubMed

Ahrens, Misha B; Huang, Kuo Hua; Narayan, Sujatha; Mensh, Brett D; Engert, Florian

2013-01-01

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features-such as turning responses to whole-field motion and dark avoidance-are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.

Utility of shallow-water ATRIS images in defining biogeologic processes and self-similarity in skeletal scleractinia, Florida reefs

USGS Publications Warehouse

Lidz, B.H.; Brock, J.C.; Nagle, D.B.

2008-01-01

A recently developed remote-sensing instrument acquires high-quality digital photographs in shallow-marine settings within water depths of 15 m. The technology, known as the Along-Track Reef-Imaging System, provides remarkably clear, georeferenced imagery that allows visual interpretation of benthic class (substrates, organisms) for mapping coral reef habitats, as intended. Unforeseen, however, are functions new to the initial technologic purpose: interpr??table evidence for real-time biogeologic processes and for perception of scaled-up skeletal self-similarity of scleractinian microstructure. Florida reef sea trials lacked the grid structure required to map contiguous habitat and submarine topography. Thus, only general observations could be made relative to times and sites of imagery. Degradation of corals was nearly universal; absence of reef fish was profound. However, ???1% of more than 23,600 sea-trial images examined provided visual evidence for local environs and processes. Clarity in many images was so exceptional that small tracks left by organisms traversing fine-grained carbonate sand were visible. Other images revealed a compelling sense, not yet fully understood, of the microscopic wall structure characteristic of scleractinian corals. Conclusions drawn from classifiable images are that demersal marine animals, where imaged, are oblivious to the equipment and that the technology has strong capabilities beyond mapping habitat. Imagery acquired along predetermined transects that cross a variety of geomorphic features within depth limits will ( 1) facilitate construction of accurate contour maps of habitat and bathymetry without need for ground-truthing, (2) contain a strong geologic component of interpreted real-time processes as they relate to imaged topography and regional geomorphology, and (3) allow cost-effective monitoring of regional- and local-scale changes in an ecosystem by use of existing-image global-positioning system coordinates to re-image areas. Details revealed in the modern setting have taphonomic implications for what is often found in the geologic record.

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.

Pacific ciguatoxins in food web components of coral reef systems in the Republic of Kiribati.

PubMed

Mak, Yim Ling; Wai, Tak-Cheung; Murphy, Margaret B; Chan, Wing Hei; Wu, Jia Jun; Lam, James C W; Chan, Leo L; Lam, Paul K S

2013-12-17

Ciguatera fish poisoning (CFP) is a foodborne illness caused by consumption of coral reef fishes contaminated by ciguatoxins (CTXs); of the known CTX congeners, the Pacific ciguatoxins (P-CTXs) are the most toxic. Little is known about the trophodynamics of P-CTXs in coral reef systems. The present study explores the distribution, transfer, and trophic magnification of P-CTX-1, -2, and -3 in coral reef systems with high (ciguatoxic) and low (reference) ciguatoxicity in a CFP-endemic nation by use of liquid chromatography-tandem mass spectrometry (LC-MS/MS). In ciguatoxic coral reef systems, P-CTXs were detected in 54% of herbivorous fishes [total P-CTXs <0.500-1670 pg/g wet weight (ww)], 72% of omnivorous fishes (<0.500-1810 pg/g ww), and 76% of carnivorous fishes (<0.500-69 500 pg/g ww), as well as a lobster ( Panulirus penicillatus ; 2.36 pg/g ww) and an octopus (Octopodidae; 2.56 pg/g ww). The dominant P-CTXs in grazers and piscivorous fishes were P-CTX-2 and -1, respectively. No significant correlation between P-CTX levels and lipid content in three target predatory fishes indicated that accumulation of P-CTXs does not depend on fat content. A weak but significant positive relationship was observed between δ(15)N and P-CTX-1 levels, but further investigation is required to confirm its biomagnification potential.

What can fish brains tell us about visual perception?

PubMed Central

Rosa Salva, Orsola; Sovrano, Valeria Anna; Vallortigara, Giorgio

2014-01-01

Fish are a complex taxonomic group, whose diversity and distance from other vertebrates well suits the comparative investigation of brain and behavior: in fish species we observe substantial differences with respect to the telencephalic organization of other vertebrates and an astonishing variety in the development and complexity of pallial structures. We will concentrate on the contribution of research on fish behavioral biology for the understanding of the evolution of the visual system. We shall review evidence concerning perceptual effects that reflect fundamental principles of the visual system functioning, highlighting the similarities and differences between distant fish groups and with other vertebrates. We will focus on perceptual effects reflecting some of the main tasks that the visual system must attain. In particular, we will deal with subjective contours and optical illusions, invariance effects, second order motion and biological motion and, finally, perceptual binding of object properties in a unified higher level representation. PMID:25324728

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...

Quaternary complexes composed of plasmid DNA/protamine/fish sperm DNA/stearic acid grafted chitosan oligosaccharide micelles for gene delivery.

PubMed

Du, Yong-Zhong; Lu, Ping; Yuan, Hong; Zhou, Jian-Ping; Hu, Fu-Qiang

2011-01-01

Quaternary complexes with condensed core of plasmid DNA, protamine, fish sperm DNA and shell of stearic acid grafted chitosan oligosaccharide (CSO-SA), were prepared. The CSO-SA could self-assemble to form nano-sized micelles in aqueous solution and demonstrated excellent internalization ability of tumor cells. Dynamic light scattering (DLS) measurement and transmission electrostatic microscope (TEM) images showed that quaternary complexes had spherical shape with about 25 nm number average diameter, and the size of quaternary complexes was smaller than that of CSO-SA micelles and CSO-SA micelles/plasmid DNA binary complexes. The transfection efficiencies of quaternary complexes on HEK293 and MCF-7 cells increased with incubation time, and were significantly higher than that of CSO-SA micelles/plasmid DNA binary complexes. The optimal transfection efficiency of quaternary complexes on HEK293 and MCF-7 cells measured by flow cytometer after 96 h was 23.82% and 41.43%, respectively. Whereas, the transfection efficiency of Lipofectamine™ 2000 on HEK293 and MCF-7 cells after 96 h was 32.45% and 33.23%, respectively. The data of luciferease activity measurement showed that the optimal ratio of plasmid DNA:fish sperm DNA:protamine:CSO-SA was 1:1:5:5. The results indicated that the present quaternary complexes were potential non-viral gene delivery system. Copyright © 2010 Elsevier B.V. All rights reserved.

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

Project Catch: A space based solution to combat illegal, unreported and unregulated fishing. Part I: Vessel monitoring system

NASA Astrophysics Data System (ADS)

Detsis, Emmanouil; Brodsky, Yuval; Knudtson, Peter; Cuba, Manuel; Fuqua, Heidi; Szalai, Bianca

2012-11-01

Space assets have a unique opportunity to play a more active role in global resource management. There is a clear need to develop resource management tools in a global framework. Illegal, Unregulated and Unreported (IUU) fishing is placing pressure on the health and size of fishing stocks around the world. Earth observation systems can provide fishery management organizations with cost effective monitoring of large swaths of ocean. Project Catch is a fisheries management project based upon the complimentary, but independent Catch-VMS and Catch-GIS systems. Catch-VMS is a Vessel Monitoring System with increased fidelity over existing offerings. Catch-GIS is a Geographical Information System that combines VMS information with existing Earth Observation data and other data sources to identify Illegal, Unregulated and Unreported (IUU) fishing. Project Catch was undertaken by 19 Masters students from the 2010 class of the International Space University. In this paper, the space-based system architecture of Project Catch is presented and analyzed. The rationale for the creation of the system, as well as the engineering trade-off studies in its creation, are discussed. The Catch-VMS proposal was envisaged in order to address two specific problems: (1) the expansion of illegal fishing to high-latitude regions where existing satellite systems coverage is an issue and (2) the lack of coverage in remote oceanic regions due to reliance on coastal-based monitoring. Catch-VMS utilizes ship-borne transponders and hosted-payload receivers on a Global Navigation Satellite System in order to monitor the position and activity of compliant fishing vessels. Coverage is global and continuous with multiple satellites in view providing positional verification through multilateration techniques. The second part of the paper briefly describes the Catch-GIS system and investigates its cost of implementation.

Use of PIT tag and underwater video recording in assessing estuarine fish movement in a high intertidal mangrove and salt marsh creek

NASA Astrophysics Data System (ADS)

Meynecke, Jan-Olaf; Poole, Geoffrey C.; Werry, Jonathan; Lee, Shing Yip

2008-08-01

We assessed movement patterns in relation to habitat availability (reflected by the extent of tidal flooding) for several commercially and recreationally important species in and out of a small mangrove creek within the subtropical Burrum River estuary (25°10'S 152°37'E) in Queensland, Australia. Movement patterns of Acanthopagrus australis, Pomadasys kaakan, Lutjanus russelli and Mugil cephalus were examined between December 2006 and April 2007 using a stationary passive integrated transponder (PIT) system adapted for saline environments (30-38 ppt) and underwater digital video cameras (DVCs). This is the second known application of a stationary PIT tag system to studying fish movement in estuarine environments. The transponder system was set in place for 104 days and recorded >5000 detections. Overall 'recapture' rate of tagged fish by the transponder system was >40%. We used PIT tags implanted in a total of 75 fish from a tidal creek connected to the main channel of the estuary. We also developed a high-resolution digital elevation (2.5 m cell size) model of the estuary derived from airborne light detection and ranging (LIDAR) and aerial imagery to estimate inundation dynamics within the tidal creek, and related the timing of inundation in various habitats to the timing of fish immigration to and emigration from the creek. Over 50% of all tagged fish were moving in and out of the creek at a threshold level when 50% of the mangrove forest became flooded. Individuals of all four species moved into and out of the tidal creek repeatedly at different times depending on species and size, indicating strong residential behaviour within the estuary. The main activity of fishes was at night time. Manual interpretation of video from >700 fish sightings at three different mangrove sites confirmed the findings of the stationary PIT system, that the function of shelter vs food in mangrove habitat may be size dependent. Our established techniques assess the spatial ecology of estuarine fish and provide important insights into fish habitat utilisation and site fidelity behaviour.

Linking ecosystems, food webs, and fish production: subsidies in salmonid watersheds

USGS Publications Warehouse

Wipfli, Mark S.; Baxter, Colden V.

2010-01-01

Physical characteristics of riverine habitats, such as large wood abundance, pool geometry and abundance, riparian vegetation cover, and surface flow conditions, have traditionally been thought to constrain fish production in these ecosystems. Conversely, the role of food resources (quantity and quality) in controlling fish production has received far less attention and consideration, though they can also be key productivity drivers. Traditional freshwater food web illustrations have typically conveyed the notion that most fish food is produced within the local aquatic habitat itself, but the concepts and model we synthesize in this article show that most fish food comes from external or very distant sources—including subsidies from marine systems borne from adult returns of anadromous fishes, from fishless headwater tributaries that transport prey to downstream fish, and from adjacent streamside vegetation and associated habitats. The model we propose further illustrates how key trophic pathways and food sources vary through time and space throughout watersheds. Insights into how food supplies affect fishes can help guide how we view riverine ecosystems, their structure and function, their interactions with marine and terrestrial systems, and how we manage natural resources, including fish, riparian habitats, and forests.

'Fish matters': the relevance of fish skin biology to investigative dermatology.

PubMed

Rakers, Sebastian; Gebert, Marina; Uppalapati, Sai; Meyer, Wilfried; Maderson, Paul; Sell, Anne F; Kruse, Charli; Paus, Ralf

2010-04-01

Fish skin is a multi-purpose tissue that serves numerous vital functions including chemical and physical protection, sensory activity, behavioural purposes or hormone metabolism. Further, it is an important first-line defense system against pathogens, as fish are continuously exposed to multiple microbial challenges in their aquatic habitat. Fish skin excels in highly developed antimicrobial features, many of which have been preserved throughout evolution, and infection defense principles employed by piscine skin are still operative in human skin. This review argues that it is both rewarding and important for investigative dermatologists to revive their interest in fish skin biology, as it provides insights into numerous fundamental issues that are of major relevance to mammalian skin. The basic molecular insights provided by zebrafish in vivo-genomics for genetic, regeneration and melanoma research, the complex antimicrobial defense systems of fish skin and the molecular controls of melanocyte stem cells are just some of the fascinating examples that illustrate the multiple potential uses of fish skin models in investigative dermatology. We synthesize the essentials of fish skin biology and highlight selected aspects that are of particular comparative interest to basic and clinically applied human skin research.

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.

OMEGAHAB-XP a bioregenerative aquatic life support system designed to be used in Bion-M1 long term space flight

NASA Astrophysics Data System (ADS)

Hilbig, Reinhard; Lebert, Michael

The OmegaHab XP Experiment will be based on the OmegaHab system successfully flown in the context of the FOTON M3 mission. OmegaHab XP -a refurbished OmegaHab for a long term mission -is in general assembled from four parts: an algae compartment, a nutrition com-partment for higher plants and crustaceens, a fish compartment and a filter compartment with biodegradant bacterias. The algae compartment (Euglena gracilis; unicellular, photosynthetic flagellate) will be illuminated with photosynthetic active radiation and will produce oxygen. The photosynthetic process also consumes carbon dioxide and if available ammonia. In addi-tion, nitrate will be taken up by the algae and by this means removed from the system. Via a gas-permeable membrane (gas/ion exchanger) the produced oxygen will be transported in a separate fish compartment. The metabolism of the fish will produce carbon dioxide and nitro-genic components. These components as well as the carbon dioxide will be transported back in the algae compartment and subsequently used by the algae. The transport of the components is enhanced by a counter flow inside the gas/ion exchanger driven by a pump. In addition, a filter system is installed which removes debris as well as ammonia by means of ammonia metabolizing bacteria. The nutrition compartment with higher plants and the crustaceans (e.g. Hyalella azteca; flown successfully aboard shuttles) builds the basis of this multi-trophic sys-tem. Hyalella azteca can reproduce in an adequate amount to replace external fish nutrition for Oreochromis mossambicus in large parts. The fish compartment is divided into two chambers: a hatchery chamber for larval fishes and an chamber for subadult Oreochromis mossambicus. The system is fully automatic and measures and stores all house-keeping data internally. These house-keeping data include light, temperature, acceleration and oxygen as well as many system related parameters. By means of Peltier-elements the system can be temperature-controlled. Two video cameras (one coupled to a sub-miniaturized microscope, one for observation of the fish) allow to monitor and internally store the behaviour of fish and algae.

Occult hemoglobin as an indicator of impingement stress in fishes

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

Not Available

1980-01-01

During the process of impingement on cooling system intake screens, fish may be subject to different types of stress, the total of which often results in the death of individual fish. This report assesses the use of occult hemoglobin in fish demand mucus as an indicator of impingement stress. (ACR)

[Aquaculture in the Netherlands: problems and perspectives].

PubMed

Hogendoorn, H

1986-11-15

New interest is being focussed on the more than 100-year-old field of fish culture in the Netherlands. The systems of production available show varying degrees of control of the fish and their environment, and they have a corresponding yield: 0.01-250 kg/m3/year. The recently developed recirculation systems (40-80 kg/m3) make possible the commercial production of luxury species of fish, independently of climatological conditions and having minimum effects on the environment. Some technical aspects of reproduction, housing, nutrition, growth, health control and marketing of the fish require further attention. But the absence of a solid tradition of fish culture is the main problem in the development of fish culture in the Netherlands today. Good fish stockmanship is required at farmers' level. And the organisation and governmental support, that turned agriculture into a highly successful industry, are also essential. For the moment, the most promising commercial prospects are provided by a number of luxury fish species: trout, salmon, eel, sole, turbot, tilapia, catfish, seabass and seabream. A joint effort may help to overcome the remaining technical and logistical uncertainties.

Rational development of an attenuated recombinant cyprinid herpesvirus 3 vaccine using prokaryotic mutagenesis and in vivo bioluminescent imaging.

PubMed

Boutier, Maxime; Ronsmans, Maygane; Ouyang, Ping; Fournier, Guillaume; Reschner, Anca; Rakus, Krzysztof; Wilkie, Gavin S; Farnir, Frédéric; Bayrou, Calixte; Lieffrig, François; Li, Hong; Desmecht, Daniel; Davison, Andrew J; Vanderplasschen, Alain

2015-02-01

Cyprinid herpesvirus 3 (CyHV 3) is causing severe economic losses worldwide in common and koi carp industries, and a safe and efficacious attenuated vaccine compatible with mass vaccination is needed. We produced single deleted recombinants using prokaryotic mutagenesis. When producing a recombinant lacking open reading frame 134 (ORF134), we unexpectedly obtained a clone with additional deletion of ORF56 and ORF57. This triple deleted recombinant replicated efficiently in vitro and expressed an in vivo safety/efficacy profile compatible with use as an attenuated vaccine. To determine the role of the double ORF56-57 deletion in the phenotype and to improve further the quality of the vaccine candidate, a series of deleted recombinants was produced and tested in vivo. These experiments led to the selection of a double deleted recombinant lacking ORF56 and ORF57 as a vaccine candidate. The safety and efficacy of this strain were studied using an in vivo bioluminescent imaging system (IVIS), qPCR, and histopathological examination, which demonstrated that it enters fish via skin infection similar to the wild type strain. However, compared to the parental wild type strain, the vaccine candidate replicated at lower levels and spread less efficiently to secondary sites of infection. Transmission experiments allowing water contamination with or without additional physical contact between fish demonstrated that the vaccine candidate has a reduced ability to spread from vaccinated fish to naïve sentinel cohabitants. Finally, IVIS analyses demonstrated that the vaccine candidate induces a protective mucosal immune response at the portal of entry. Thus, the present study is the first to report the rational development of a recombinant attenuated vaccine against CyHV 3 for mass vaccination of carp. We also demonstrated the relevance of the CyHV 3 carp model for studying alloherpesvirus transmission and mucosal immunity in teleost skin.

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

Definition of MYC genetic heteroclonality in diffuse large B-cell lymphoma with 8q24 rearrangement and its impact on protein expression.

PubMed

Valera, Alexandra; Epistolio, Samantha; Colomo, Lluis; Riva, Alice; Balagué, Olga; Dlouhy, Ivan; Tzankov, Alexandar; Bühler, Marco; Haralambieva, Eugenia; Campo, Elias; Soldini, Davide; Mazzucchelli, Luca; Martin, Vittoria

2016-08-01

MYC rearrangement can be detected in a subgroup of diffuse large B-cell lymphoma characterized by unfavorable prognosis. In contrast to Burkitt lymphoma, the correlation between MYC rearrangement and MYC protein expression in diffuse large B-cell lymphoma is less clear, as approximately one-third of rearranged cases show negative or low expression by immunohistochemistry. To better understand whether specific characteristics of the MYC rearrangement may influence its protein expression, we investigated 43 de novo diffuse large B-cell lymphoma positive for 8q24 rearrangement by FISH, using 14 Burkitt lymphoma for comparison. Different cell populations (clones), breakpoints (classical vs non-classical FISH patterns), partner genes (IGH vs non-IGH) and immunostaining were detected and analyzed using computerized image systems. In a subgroup of diffuse large B-cell lymphoma, we observed different clones within the same tumor distinguishing the founder clone with MYC rearrangement alone from other subclones, carrying MYC rearrangement coupled with loss/extra copies of derivatives/normal alleles. This picture, which we defined MYC genetic heteroclonality, was found in 42% of cases and correlated to negative MYC expression (P=0.026). Non-classical FISH breakpoints were detected in 16% of diffuse large B-cell lymphoma without affecting expression (P=0.040). Non-IGH gene was the preferential partner of rearrangement in those diffuse large B-cell lymphoma showing MYC heteroclonality (P=0.016) and/or non-classical FISH breakpoints (P=0.058). MYC heteroclonality was not observed in Burkitt lymphoma and all cases had positive MYC expression. Non-classical FISH MYC breakpoint and non-IGH partner were found in 29 and 20% of Burkitt lymphoma, respectively. In conclusion, MYC genetic heteroclonality is a frequent event in diffuse large B-cell lymphoma and may have a relevant role in modulating MYC expression.

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.

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.

Historical changes in Nebraska's lotic fish assemblages: Implications of anthropogenic alterations

USGS Publications Warehouse

Smith, Christopher D.; Fischer, Jesse R.; Quist, Michael C.

2014-01-01

The plains of midwestern North America have undergone significant anthropogenic alterations following European settlement with consequent effects to lotic fish assemblage structure. We examined trends in fish assemblage structure and function in Nebraska's lotic systems using site-specific, presence-absence data from historical (1939–1940) and contemporary surveys (2003–2005; n  =  183). Shifts in fish assemblage structure were characterized by declines of specialist species (e.g., western silvery minnow Hybognathus argyritis) and increases in nonnative, sport, and generalist species (e.g., common carp Cyprinus carpio). Our research illustrates differences between historical and contemporary surveys for both taxonomic and functional metrics. Changes in fish assemblage structure were correlated with a contemporary measure of anthropogenic alteration (Human Threat Index; HTI) and were most pronounced for large-scale threats (i.e., watershed HTI, overall HTI). The HTI is a composite index of cumulative anthropogenic alterations experienced by a stream system and was used to investigate broad-scale implications of anthropogenic activity on fish assemblage structure. Fish assemblages among sites were more similar in contemporary surveys than in historical surveys, such changes might indicate a homogenization of the fish assemblages. Losses of native species and increases in introduced species have occurred in Nebraska's lotic systems across a broad temporal span and shifts are likely related to high levels of human perturbation.

Unintended consequences and trade-offs of fish passage

USGS Publications Warehouse

McLaughlin, Robert L.; Smyth, Eric R.; Castro-Santos, Theodore; Jones, Michael L.; Koops, Marten A.; Pratt, Thomas C.; Vélez-Espino, Luis-Antonio

2012-01-01

We synthesized evidence for unintended consequences and trade-offs associated with the passage of fishes. Provisioning of fish passageways at dams and dam removals are being carried out increasingly as resource managers seek ways to reduce fragmentation of migratory fish populations and restore biodiversity and nature-like ecosystem services in tributaries altered by dams. The benefits of provisioning upstream passage are highlighted widely. Possible unwanted consequences and trade-offs of upstream passage are coming to light, but remain poorly examined and underappreciated. Unintended consequences arise when passage of native and desirable introduced fishes is delayed, undone (fallback), results in patterns of movement and habitat use that reduce Darwinian fitness (e.g. ecological traps), or is highly selective taxonomically and numerically. Trade-offs arise when passage decisions intended to benefit native species interfere with management decisions intended to control the unwanted spread of non-native fishes and aquatic invertebrates, or genes, diseases and contaminants carried by hatchery and wild fishes. These consequences and trade-offs will vary in importance from system to system and can result in large economic and environmental costs. For some river systems, decisions about how to manage fish passage involve substantial risks and could benefit from use of a formal, structured process that allows transparent, objective and, where possible, quantitative evaluation of these risks. Such a process can also facilitate the design of an adaptive framework that provides valuable insights into future decisions.

Model of an aquaponic system for minimised water, energy and nitrogen requirements.

PubMed

Reyes Lastiri, D; Slinkert, T; Cappon, H J; Baganz, D; Staaks, G; Keesman, K J

2016-01-01

Water and nutrient savings can be established by coupling water streams between interacting processes. Wastewater from production processes contains nutrients like nitrogen (N), which can and should be recycled in order to meet future regulatory discharge demands. Optimisation of interacting water systems is a complex task. An effective way of understanding, analysing and optimising such systems is by applying mathematical models. The present modelling work aims at supporting the design of a nearly emission-free aquaculture and hydroponic system (aquaponics), thus contributing to sustainable production and to food security for the 21st century. Based on the model, a system that couples 40 m(3) fish tanks and a hydroponic system of 1,000 m(2) can produce 5 tons of tilapia and 75 tons of tomato yearly. The system requires energy to condense and recover evaporated water, for lighting and heating, adding up to 1.3 GJ/m(2) every year. In the suggested configuration, the fish can provide about 26% of the N required in a plant cycle. A coupling strategy that sends water from the fish to the plants in amounts proportional to the fish feed input, reduces the standard deviation of the NO3(-) level in the fish cycle by 35%.

Evaluation of Aquaponics Techniques for Enhancing Productivity and Degree of Closure of Bioregenerative Life Support Systems (BLSS)

NASA Astrophysics Data System (ADS)

Nelson, Mark; Dempster, William; Highfield, Eric

A number of researchers in space bioregenerative life support systems (BLSS) have advocated the inclusion of fish-rearing. Fish have relatively high feed to production ratios and can utilize some waste products from other system components. In recent years, there has been much advance in an approach to combining fish-culture with hydroponically-grown crops called “aquaponics”. Aquaponics systems vary but generally include: fish-rearing unit, settling basin, biofilter, hydroponic plant unit and sump where water is pumped back and the cycle continues. Aquaponics research and application has grown since these systems have the potential to increase overall productivity of both crops and fish. Since the fish waste is used as the growth medium of the food plants, there are environmental benefits in reduced discharge of nutrient-rich wastewater which has been one of the drawbacks of conventional aquaculture. In addition, since water use is reduced 95+% over field agriculture, since water from the hydroponic tanks is fed back to the fish tanks and water is recycled apart from evapotranspiration losses, conservation of water resources and applications in water-limited arid regions are other benefits fueling the spread of aquaponics around the world. These considerations also make utilization of aquaponic approaches desirable in BLSS for space application. This paper will examine some recent research results with aquaponics and explore how it might be utilized for food production and reduction of consumables in space life support. In addition, a review and comparison with other fish-culture options previously advanced will evaluate whether aquaponics can improve production efficiency, reduce inputs and better recycle critical resources. Finally, we will explore whether for the space environment, even more advanced aquaponics systems are possible where consumables such as fish-food can be partially or completely supplied from other subsystems of the BLSS and ET water losses compensated by condensation from humidity in the atmosphere. For longer term space life support, the paper will evaluate how aquaponics might integrate soil-like-substrate made from inedible crop biomass, utilize algae (edible) for water quality improvement in the fish tanks and how any wastes might be more fully integrated in other BLSS subsystems to improve overall closure ratio.

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.

One-Minute Fish Freshness Evaluation by Testing the Volatile Amine Gas with an Ultrasensitive Porous-Electrode-Capped Organic Gas Sensor System.

PubMed

Chang, Liang-Yu; Chuang, Ming-Yen; Zan, Hsiao-Wen; Meng, Hsin-Fei; Lu, Chia-Jung; Yeh, Ping-Hung; Chen, Jian-Nan

2017-04-28

In this work, we successfully demonstrate a fast method to determine the fish freshness by using a sensing system containing an ultrasensitive amine gas sensor to detect the volatile amine gas from the raw fish meat. When traditional titration method takes 4 h and complicated steps to test the total volatile basic nitrogen (TVB-N) as a worldwide standard for fish freshness, our sensor takes 1 min to deliver an electrical sensing response that is highly correlated with the TVB-N value. When detecting a fresh fish with a TVB-N as 18 mg/100 g, the sensor delivers an effective ammonia concentration as 100 ppb. For TVB-N as 28-35 mg/100 g, a well-accepted freshness limit, the effective ammonia concentration is as 200-300 ppb. The ppb-regime sensitivity of the sensor and the humidity control in the sensing system are the keys to realizing fast and accurate detection. It is expected that the results in this report enable the development of on-site freshness detection and real-time monitoring in a fish factory.

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.

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.

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.

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.

A Review of Artificial Lateral Line in Sensor Fabrication and Bionic Applications for Robot Fish.

PubMed

Liu, Guijie; Wang, Anyi; Wang, Xinbao; Liu, Peng

2016-01-01

Lateral line is a system of sense organs that can aid fishes to maneuver in a dark environment. Artificial lateral line (ALL) imitates the structure of lateral line in fishes and provides invaluable means for underwater-sensing technology and robot fish control. This paper reviews ALL, including sensor fabrication and applications to robot fish. The biophysics of lateral line are first introduced to enhance the understanding of lateral line structure and function. The design and fabrication of an ALL sensor on the basis of various sensing principles are then presented. ALL systems are collections of sensors that include carrier and control circuit. Their structure and hydrodynamic detection are reviewed. Finally, further research trends and existing problems of ALL are discussed.

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.

The paraty artisanal fishery (southeastern Brazilian coast): ethnoecology and management of a social-ecological system (SES)

PubMed Central

2012-01-01

This study intends to give recommendations to the management of Paraty fishery in Brazil through an interplay of local and scientific knowledge. In particular, the objectives are the following: 1) to describe the Paraty fishery; 2) to compare the fishermen’s local ecological knowledge with recorded fish landings and previous studies in Paraty; 3) to combine the data on local fishing and on local/Caiçara livelihoods with the SES (social-ecological systems) Model. The methods include a systematic survey of fishing in Tarituba and Praia Grande, which are located in the northern end and the central part of the Paraty municipality, respectively. For four days each month, systematic data on catches at landing points were collected, as well as macroscopic gonad analysis data for the fishes Centropomus parallelus and C. undecimalis (snook, robalo), Epinephelus marginatus (grouper, garoupa), Scomberomorus cavalla (King mackerel, cavala), and Lutjanus synagris (Lane snapper, vermelho). Spring and summer are important seasons during which some species reproduce, and the integration of fishing periods for some target species could assist in fishing management through the use of closed seasons. Fishermen could obtain complementary earnings from tourism and from the “defeso system” (closed season including a salary payment) to conserve fishing stocks. The SES model facilitates an understanding of the historical context of fishing, its economic importance for local livelihoods, the constraints from conservation measures that affect fishermen, and the management processes that already exist, such as the defeso. If used to integrate fishing with complementary activities (tourism), such a system could improve the responsibility of fishermen regarding the conservation of fish stocks. PMID:22738073

Modification and Extension of the Environmental Technical Information System (ETIS) for the Air Force

DTIC Science & Technology

1979-12-01

OF SYSTEMS ............ 26 Ai CONCLUSIONS AND RECOMMENDATIONS.............................. 28 fa Conclusions Recommendations REFERENCES 30 APPENDiX A...Large Lake Fishing J_ 30 . Coastal Water Fishing 31. She! fish 32. Deep-Sea Fishing 33. Disease Vectors EE- -34. Noxious Weeds 35. Other Undesirable...7,132 9.5 20-24 1239 0 1239 33.4 16 17 33 3.4 2.984 3,201 6,185 8.2 25-29 803 111 914 24.7 29 30 59 6.1 2,425 2,511 4,936 6.6 30 -34 470 43 513 13.8 62

1. FIRST SECTION OF PIPELINE BETWEEN CONFLUENCE POOL AND FISH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. FIRST SECTION OF PIPELINE BETWEEN CONFLUENCE POOL AND FISH SCREEN. NOTE RETAINING WALL BESIDE PIPE. VIEW TO NORTH-NORTHEAST. - Santa Ana River Hydroelectric System, Pipeline to Fish Screen, Redlands, San Bernardino County, CA

B-Transform and Its Application to a Fish-Hyacinth Model

ERIC Educational Resources Information Center

Oyelami, B. O.; Ale, S. O.

2002-01-01

A new transform proposed by Oyelami and Ale for impulsive systems is applied to an impulsive fish-hyacinth model. A biological policy regarding the growth of the fish and the hyacinth populations is formulated.

NPDES Permit for Leadville National Fish Hatchery in Colorado

EPA Pesticide Factsheets

Under National Pollutant Discharge Elimination System permit number CO-0000582, the U.S. Department of the Interior, Fish and Wildlife Service is authorized to discharge from its Leadville National Fish Hatchery wastewater treatment facility in Colorado.

Physiological basis of climate change impacts on North American inland fishes

USGS Publications Warehouse

Whitney, James E.; Al-Chokhachy, Robert K.; Bunnell, David B.; Caldwell, Colleen A.; Cooke, Steven J.; Eliason, Erika J.; Rogers, Mark W.; Lynch, Abigail J.; Paukert, Craig P.

2016-01-01

Global climate change is altering freshwater ecosystems and affecting fish populations and communities. Underpinning changes in fish distribution and assemblage-level responses to climate change are individual-level physiological constraints. In this review, we synthesize the mechanistic effects of climate change on neuroendocrine, cardiorespiratory, immune, osmoregulatory, and reproductive systems of freshwater and diadromous fishes. Observed climate change effects on physiological systems are varied and numerous, including exceedance of critical thermal tolerances, decreased cardiorespiratory performance, compromised immune function, and altered patterns of individual reproductive investment. However, effects vary widely among and within species because of species, population, and even sex-specific differences in sensitivity and resilience and because of habitat-specific variation in the magnitude of climate-related environmental change. Research on the interactive effects of climate change with other environmental stressors across a broader range of fish diversity is needed to further our understanding of climate change effects on fish physiology.

Status of native stream fishes within selected protected areas of Niobrara River in western Nebraska

USGS Publications Warehouse

Spurgeon, Jonathan J.; Stasiak, Richard H.; Cunningham, George R.; Pope, Kevin L.; Pegg, Mark A.

2014-01-01

Lotic systems within the Great Plains are characterized by highly fluctuating conditions through both space and time. Fishes inhabiting these systems have adopted specific life-history strategies to survive in such environments; however, anthropogenic disturbance to prairie streams has resulted in declines and extirpation of many native stream fishes. Terrestrial protected areas (i.e., parks and reserves) are designated to support native flora and fauna and, it is assumed, to provide protection to native fishes. We assessed the presence and relative abundance of stream fish populations within protected areas along the Niobrara River in western Nebraska based on data collected during 1979, 1989, 2008, and 2011. The spatial extent of protection, landscape changes resulting in degraded physiochemical parameters, and introduced species may reduce the effectiveness of these terrestrial protected areas in protecting native fishes in Great Plains stream environments.

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).

A novel system for embryo-larval toxicity testing of pelagic fish: Applications for impact assessment of Deepwater Horizon crude oil.

PubMed

Stieglitz, John D; Mager, Edward M; Hoenig, Ronald H; Alloy, Matthew; Esbaugh, Andrew J; Bodinier, Charlotte; Benetti, Daniel D; Roberts, Aaron P; Grosell, Martin

2016-11-01

Key differences in the developmental process of pelagic fish embryos, in comparison to embryos of standard test fish species, present challenges to obtaining sufficient control survival needed to successfully perform traditional toxicity testing bioassays. Many of these challenges relate to the change in buoyancy, from positive to negative, of pelagic fish embryos that occurs just prior to hatch. A novel exposure system, the pelagic embryo-larval exposure chamber (PELEC), has been developed to conduct successful bioassays on the early life stages (ELSs; embryos/larvae) of pelagic fish. Using this unique recirculating upwelling system, it was possible to significantly improve control survival in pelagic fish ELS bioassays compared to commonly used static exposure methods. Results demonstrate that control performance of mahi-mahi (Coryphaena hippurus) embryos in the PELEC system, measured as percent survival after 96-hrs, significantly outperformed agitated static exposure and static exposure systems. Similar significant improvements in 72-hr control survival were obtained with yellowfin tuna (Thunnus albacares). The PELEC system was subsequently used to test the effects of photo-induced toxicity of crude oil to mahi-mahi ELSs over the course of 96-hrs. Results indicate a greater than 9-fold increase in toxicity of Deepwater Horizon (DWH) crude oil during co-exposure to ambient sunlight compared to filtered ambient sunlight, revealing the importance of including natural sunlight in 96-hr DWH crude oil bioassays as well as the PELEC system's potential application in ecotoxicological assessments. Copyright © 2016 Elsevier Ltd. All rights reserved.

50 CFR 622.373 - Limited access system for charter vessel/headboat permits for Gulf coastal migratory pelagic fish.

Code of Federal Regulations, 2013 CFR

2013-10-01

.../headboat permits for Gulf coastal migratory pelagic fish. 622.373 Section 622.373 Wildlife and Fisheries... for Gulf coastal migratory pelagic fish. (a) No applications for additional charter vessel/headboat permits for Gulf coastal migratory pelagic fish will be accepted. Existing permits may be renewed, are...

50 CFR 622.373 - Limited access system for charter vessel/headboat permits for Gulf coastal migratory pelagic fish.

Code of Federal Regulations, 2014 CFR

2014-10-01

.../headboat permits for Gulf coastal migratory pelagic fish. 622.373 Section 622.373 Wildlife and Fisheries... for Gulf coastal migratory pelagic fish. (a) No applications for additional charter vessel/headboat permits for Gulf coastal migratory pelagic fish will be accepted. Existing permits may be renewed, are...

A model describing the effect of sex-reversed YY fish in an established wild population: The use of a Trojan Y chromosome to cause extinction of an introduced exotic species.

PubMed

Gutierrez, Juan B; Teem, John L

2006-07-21

A novel means of inducing extinction of an exotic fish population is proposed using a genetic approach to shift the ratio of male to females within a population. In the proposed strategy, sex-reversed fish containing two Y chromosomes are introduced into a normal fish population. These YY fish result in the production of a disproportionate number of male fish in subsequent generations. Mathematical modeling of the system following introduction of YY fish at a constant rate reveals that female fish decline in numbers over time, leading to eventual extinction of the population.

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.

Different binarization processes validated against manual counts of fluorescent bacterial cells.

PubMed

Tamminga, Gerrit G; Paulitsch-Fuchs, Astrid H; Jansen, Gijsbert J; Euverink, Gert-Jan W

2016-09-01

State of the art software methods (such as fixed value approaches or statistical approaches) to create a binary image of fluorescent bacterial cells are not as accurate and precise as they should be for counting bacteria and measuring their area. To overcome these bottlenecks, we introduce biological significance to obtain a binary image from a greyscale microscopic image. Using our biological significance approach we are able to automatically count about the same number of cells as an individual researcher would do by manual/visual counting. Using the fixed value or statistical approach to obtain a binary image leads to about 20% less cells in automatic counting. In our procedure we included the area measurements of the bacterial cells to determine the right parameters for background subtraction and threshold values. In an iterative process the threshold and background subtraction values were incremented until the number of particles smaller than a typical bacterial cell is less than the number of bacterial cells with a certain area. This research also shows that every image has a specific threshold with respect to the optical system, magnification and staining procedure as well as the exposure time. The biological significance approach shows that automatic counting can be performed with the same accuracy, precision and reproducibility as manual counting. The same approach can be used to count bacterial cells using different optical systems (Leica, Olympus and Navitar), magnification factors (200× and 400×), staining procedures (DNA (Propidium Iodide) and RNA (FISH)) and substrates (polycarbonate filter or glass). Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Possible return of Acropora cervicornis at Pulaski Shoal, Dry Tortugas National Park, Florida

USGS Publications Warehouse

Lidz, Barbara H.; Zawada, David G.

2013-01-01

Seabed classification is essential to assessing environmental associations and physical status in coral reef ecosystems. At Pulaski Shoal in Dry Tortugas National Park, Florida, nearly continuous underwater-image coverage was acquired in 15.5 hours in 2009 along 70.2 km of transect lines spanning ~0.2 km2. The Along-Track Reef-Imaging System (ATRIS), a boat-based, high-speed, digital imaging system, was used. ATRIS-derived benthic classes were merged with a QuickBird satellite image to create a habitat map that defines areas of senile coral reef, carbonate sand, seagrasses, and coral rubble. This atypical approach of starting with extensive, high-resolution in situ imagery and extrapolating between transect lines using satellite imagery leverages the strengths of each remote-sensing modality. The ATRIS images also captured the spatial distribution of two species once common on now-degraded Florida-Caribbean coral reefs: the stony staghorn coral Acropora cervicornis, a designated threatened species, and the long-spined urchin Diadema antillarum. This article documents the utility of ATRIS imagery for quantifying number and estimating age of A. cervicornis colonies (n = 400, age range, 5–11 y) since the severe hypothermic die-off in the Dry Tortugas in 1976–77. This study is also the first to document the largest number of new colonies of A. cervicornis tabulated in an area of the park where coral-monitoring stations maintained by the Fish and Wildlife Research Institute have not been established. The elevated numbers provide an updated baseline for tracking revival of this species at Pulaski Shoal.

Measuring the performance of two stationary interrogation systems for detecting downstream and upstream movement of PIT-tagged salmonids

USGS Publications Warehouse

Connolly, P.J.; Jezorek, I.G.; Martens, K.D.; Prentice, E.F.

2008-01-01

We tested the performance of two stationary interrogation systems designed for detecting the movement of fish with passive integrated transponder (PIT) tags. These systems allowed us to determine the direction of fish movement with high detection efficiency and high precision in a dynamic stream environment. We describe an indirect method for deriving an estimate for detection efficiency and the associated variance that does not rely on a known number of fish passing the system. By using six antennas arranged in a longitudinal series of three arrays, we attained detection efficiencies for downstream- and upstream-moving fish exceeding 96% during high-flow periods and approached 100% during low-flow periods for the two interrogation systems we tested. Because these systems did not rely on structural components, such as bridges or culverts, they were readily adaptable to remote, natural stream sites. Because of built-in redundancy, these systems were able to perform even with a loss of one or more antennas owing to dislodgement or electrical failure. However, the reduction in redundancy resulted in decreased efficiency and precision and the potential loss of ability to determine the direction of fish movement. What we learned about these systems should be applicable to a wide variety of other antenna configurations and to other types of PIT tags and transceivers.

Fish trypsins: potential applications in biomedicine and prospects for production.

PubMed

Jesús-de la Cruz, Kristal; Álvarez-González, Carlos Alfonso; Peña, Emyr; Morales-Contreras, José Antonio; Ávila-Fernández, Ángela

2018-04-01

In fishes, trypsins are adapted to different environmental conditions, and the biochemical and kinetic properties of a broad variety of native isoforms have been studied. Proteolytic enzymes remain in high demand in the detergent, food, and feed industries; however, our analysis of the literature showed that, in the last decade, some fish trypsins have been studied for the synthesis of industrial peptides and for specific biomedical uses as antipathogenic agents against viruses and bacteria, which have been recently patented. In addition, innovative strategies of trypsin administration have been studied to ensure that trypsins retain their properties until they exert their action. Biomedical uses require the production of high-quality enzymes. In this context, the production of recombinant trypsins is an alternative. For this purpose, E. coli -based systems have been tested for the production of fish trypsins; however, P. pastoris -based systems also seem to show great potential in the production of fish trypsins with higher production quality. On the other hand, there is a lack of information regarding the specific structures, biochemical and kinetic properties, and characteristics of trypsins produced using heterologous systems. This review describes the potential uses of fish trypsins in biomedicine and the enzymatic and structural properties of native and recombinant fish trypsins obtained to date, outlining some prospects for their study.

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish.

PubMed

Kuz'mina, V V; Skvortsova, E G; Shalygin, M V; Kovalenko, K E

2015-12-01

Many fish enzymatic systems possess limited adaptations to low temperature; however, little data are available to judge whether enzymes of fish prey and intestinal microbiota can mitigate this deficiency. In this study, the activity of serine peptidases (casein-lytic, mainly trypsin and hemoglobin-lytic, mainly chymotrypsin) of intestinal mucosa, chyme and intestinal microflora in four species of planktivorous (blue bream) and benthivorous (roach, crucian carp, perch) was investigated across a wide temperature range (0-70 °C) to identify adaptations to low temperature. At 0 °C, the relative activity of peptidases of intestinal mucosa (<13%) and usually intestinal microflora (5-12.6%) is considerably less than that of chyme peptidases (up to 40% of maximal activity). The level of peptidase relative activity in crucian carp intestinal microflora was 45% of maximal activity. The shape of t°-function curves of chyme peptidase also differs in fish from different biotopes. Fish from the littoral group are characterized by a higher degree of adaptation of chyme casein-lytic peptidases to functioning at low temperatures as compared to fish from the pelagic group. The role of intestinal microbiota and prey peptidases in digestive system adaptations of planktivorous and benthivorous fish to low temperatures is discussed.

Exploiting 16S rRNA gene for the detection and quantification of fish as a potential allergenic food: A comparison of two real-time PCR approaches.

PubMed

Fernandes, Telmo J R; Costa, Joana; Oliveira, M Beatriz P P; Mafra, Isabel

2018-04-15

Fish is one of the most common allergenic foods that should be accurately labelled to protect the health of allergic consumers. In this work, two real-time PCR systems based on the EvaGreen dye and a TaqMan probe are proposed and compared. New primers were designed to target the 16S rRNA gene, as a universal maker for fish detection, with fully demonstrated specificity for a wide range of fish species. Both systems showed similar absolute sensitivities, down to 0.01 pg of fish DNA, and adequate real-time PCR performance parameters. The probe system showed higher relative sensitivity and dynamic range (0.0001-50%) than the EvaGreen (0.05-50%). They were both precise, but trueness was compromised at the highest tested level with the EvaGreen assay. Therefore, both systems were successful, although the probe one exhibited the best performance. Its application to verify labelling compliance of foodstuffs suggested a high level of mislabelling and/or fraudulent practices. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Fisheries management impacts on target species status

PubMed Central

Melnychuk, Michael C.; Peterson, Emily; Elliott, Matthew; Hilborn, Ray

2017-01-01

Fisheries management systems around the world are highly diverse in their design, operation, and effectiveness at meeting objectives. A variety of management institutions, strategies, and tactics are used across disparate regions, fishing fleets, and taxonomic groups. At a global level, it is unclear which particular management attributes have greatest influence on the status of fished populations, and also unclear which external factors affect the overall success of fisheries management systems. We used expert surveys to characterize the management systems by species of 28 major fishing nations and examined influences of economic, geographic, and fishery-related factors. A Fisheries Management Index, which integrated research, management, enforcement, and socioeconomic attributes, showed wide variation among countries and was strongly affected by per capita gross domestic product (positively) and capacity-enhancing subsidies (negatively). Among 13 management attributes considered, three were particularly influential in whether stock size and fishing mortality are currently in or trending toward desirable states: extensiveness of stock assessments, strength of fishing pressure limits, and comprehensiveness of enforcement programs. These results support arguments that the key to successful fisheries management is the implementation and enforcement of science-based catch or effort limits, and that monetary investment into fisheries can help achieve management objectives if used to limit fishing pressure rather than enhance fishing capacity. Countries with currently less-effective management systems have the greatest potential for improving long-term stock status outcomes and should be the focus of efforts to improve fisheries management globally. PMID:27994155

Fisheries management impacts on target species status.

PubMed

Melnychuk, Michael C; Peterson, Emily; Elliott, Matthew; Hilborn, Ray

2017-01-03

Fisheries management systems around the world are highly diverse in their design, operation, and effectiveness at meeting objectives. A variety of management institutions, strategies, and tactics are used across disparate regions, fishing fleets, and taxonomic groups. At a global level, it is unclear which particular management attributes have greatest influence on the status of fished populations, and also unclear which external factors affect the overall success of fisheries management systems. We used expert surveys to characterize the management systems by species of 28 major fishing nations and examined influences of economic, geographic, and fishery-related factors. A Fisheries Management Index, which integrated research, management, enforcement, and socioeconomic attributes, showed wide variation among countries and was strongly affected by per capita gross domestic product (positively) and capacity-enhancing subsidies (negatively). Among 13 management attributes considered, three were particularly influential in whether stock size and fishing mortality are currently in or trending toward desirable states: extensiveness of stock assessments, strength of fishing pressure limits, and comprehensiveness of enforcement programs. These results support arguments that the key to successful fisheries management is the implementation and enforcement of science-based catch or effort limits, and that monetary investment into fisheries can help achieve management objectives if used to limit fishing pressure rather than enhance fishing capacity. Countries with currently less-effective management systems have the greatest potential for improving long-term stock status outcomes and should be the focus of efforts to improve fisheries management globally.

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/

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.

Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches.

PubMed

Yousef Kalafi, Elham; Tan, Wooi Boon; Town, Christopher; Dhillon, Sarinder Kaur

2016-12-22

Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods. Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%. The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented.

Application of the BAX for screening/genus Listeria polymerase chain reaction system for monitoring Listeria species in cold-smoked fish and in the smoked fish processing environment.

PubMed

Norton, D M; McCamey, M; Boor, K J; Wiedmann, M

2000-03-01

The cold-smoked fish industry was used as a model for the development of a system for monitoring Listeria spp. in foods and in the food processing environment. A total of 214 samples including raw fish, fish during the cold-smoking process, finished product, and environmental samples were collected from three processing facilities over two visits to each facility. Samples were screened for Listeria spp. using the BAX for Screening/genus Listeria polymerase chain reaction system (PCR) and by culture. Listeria spp., confirmed by the API Listeria test strip or by a PCR assay targeting the L. monocytogenes hlyA gene, were isolated from a total of 89 (41.6%) samples. Of these, 80 samples also tested positive for Listeria spp. using the BAX system. Specifically, 42 (55.3%) environmental samples (n = 76), 11 (25.6%) raw materials samples (n = 43), 20 (35.1%) samples from fish in various stages of processing (n = 57), and 7 (18.4%) finished product samples (n = 38) tested positive for Listeria spp. using the BAX system. Five (4.0%) of the 125 culture-negative samples yielded BAX system-positive results. Listeria isolates from each of nine culture-positive/BAX system-negative samples yielded a positive reaction when tested in pure culture by the BAX system, suggesting that our false-negative results were likely due to the presence of low Listeria numbers in the initial enrichment as opposed to nonreacting isolates. The employment of alternative enrichment protocols, such as the two-step enrichment recommended by the manufacturer, may increase the sensitivity of the assay.

Fluorescence enhancement of quercetin complexes by silver nanoparticles and its analytical application

NASA Astrophysics Data System (ADS)

Liu, Ping; Zhao, Liangliang; Wu, Xia; Huang, Fei; Wang, Minqin; Liu, Xiaodan

2014-03-01

It is found that the plasmon effect of silver nanoparticles (AgNPs) helps to enhance the fluorescence intensity of the quercetin (Qu) and nucleic acids system. Qu exhibited strong fluorescence enhancement when it bound to nucleic acids in the presence of AgNPs. Based on this, a sensitive method for the determination of nucleic acids was developed. The detection limits for the nucleic acids (S/N = 3) were reduced to the ng mL-1 level. The interaction mechanism of the AgNPs-fish sperm DNA (fsDNA)-Qu system was also investigated in this paper. This complex system of Qu and AgNPs was also successfully used for the detection of nucleic acids in agarose gel electrophoresis analysis. Preliminary results indicated that AgNPs also helped to improve sensitivity in the fluorescence image analysis of Qu combined with cellular contents in Arabidopsis thaliana protoplasts.

Spatial patterns of fish communities along two estuarine gradients in southern Florida

USGS Publications Warehouse

Green, D.P.J.; Trexler, J.C.; Lorenz, J.J.; McIvor, C.C.; Philippi, T.

2006-01-01

In tropical and subtropical estuaries, gradients of primary productivity and salinity are generally invoked to explain patterns in community structure and standing crops of fishes. We documented spatial and temporal patterns in fish community structure and standing crops along salinity and nutrient gradients in two subtropical drainages of Everglades National Park, USA. The Shark River drains into the Gulf of Mexico and experiences diurnal tides carrying relatively nutrient enriched waters, while Taylor River is more hydrologically isolated by the oligohaline Florida Bay and experiences no discernable lunar tides. We hypothesized that the more nutrient enriched system would support higher standing crops of fishes in its mangrove zone. We collected 50 species of fish from January 2000 to April 2004 at six sampling sites spanning fresh to brackish salinities in both the Shark and Taylor River drainages. Contrary to expectations, we observed lower standing crops and density of fishes in the more nutrient rich tidal mangrove forest of the Shark River than in the less nutrient rich mangrove habitats bordering the Taylor River. Tidal mangrove habitats in the Shark River were dominated by salt-tolerant fish and displayed lower species richness than mangrove communities in the Taylor River, which included more freshwater taxa and yielded relatively higher richness. These differences were maintained even after controlling for salinity at the time of sampling. Small-scale topographic relief differs between these two systems, possibly created by tidal action in the Shark River. We propose that this difference in topography limits movement of fishes from upstream marshes into the fringing mangrove forest in the Shark River system, but not the Taylor River system. Understanding the influence of habitat structure, including connectivity, on aquatic communities is important to anticipate effects of construction and operational alternatives associated with restoration of the Everglades ecosystem.

Effects of temperature on Veronaea botryosa infections in white sturgeon Acipenser transmontanus and fungal induced cytotoxicity of fish cell lines.

PubMed

Coleman, Denver J; Camus, Alvin C; Martínez-López, Beatriz; Yun, Susan; Stevens, Brittany; Soto, Esteban

2018-02-01

Veronaea botryosa is a melanized mold and cause of systemic fungal infections in cultured sturgeon (Acipenser spp.). Mortality in adult female sturgeon caused by this emergent pathogen results in significant economic losses for the caviar industry. Little is known regarding environmental conditions conducive to V. botryosa infection. This study evaluated the effect of temperature on V. botryosa infectivity and dissemination following intramuscular injection challenge of white sturgeon maintained at 13 or 18 °C for 40 days. Daily mortality was recorded and persistence of the fungus in the livers of moribund and surviving fish was investigated using culture and histopathological analysis. Fish maintained at 18 °C developed systemic phaeohyphomycosis and had significantly greater mortality than controls and fish maintained at 13 °C (p < 0.05). Challenged fish, regardless of temperature, exhibited lesions in multiple organs. However, muscle lesions, angioinvasion, and systemic dissemination were more severe and widespread in fish challenged at the higher temperature. In vitro cytotoxicity of V. botryosa was evaluated in white sturgeon skin (WSSK-1) and epithelioma papulosum cyprini (EPC) cell lines inoculated at spore:cell ratios of 1:10, 1:1 and 10:1, then incubated 15, 20 and 25 °C. Cytotoxicity, as indicated by quantifying the release of lactate dehydrogenase into culture supernatants, increased with increasing spore dose and incubation temperature in both fish cell lines. Findings suggest that temperature significantly influences the development of systemic V. botryosa infection in white sturgeon and that WSSK-1 and EPC cells are suitable in vitro models for the study of host-pathogen interactions between V. botryosa and fish epithelial cells.