Fish Screens Research Articles

A unique epithelioid vascular neoplasm of bone characterized by EWSR1/FUS-NFATC1/2 fusions.

An increasing number of epithelioid vascular lesions, in particular tumors from the benign and low-grade end of the spectrum, have been characterized by recurrent gene fusions. As a result, the detection of these molecular markers have improved the classification of diagnostically challenging cases. However, despite the significant progress, there are occasional lesions that do not fit in known histologic or molecular groups. Herein, we present five such unclassified epithelioid vascular lesions, which occurred in the bone and showed a distinct morphology composed of alternating vasoformative and solid growth and mild to moderate nuclear pleomorphism. The variegated morphologic appearance resembled that of composite hemangioendothelioma, being distinct from both epithelioid hemangioma and epithelioid hemangioendothelioma, and consistently showed cytologic atypia. Due to their unusual morphologic appearance and negative molecular work-up, targeted transcriptome sequencing was performed in two cases showing the presence of NFATC2 fusions with either EWSR1 or FUS genes. Three additional bone tumors with EWSR1 gene rearrangements were identified by FISH screening of a large cohort of 45 fusion-negative epithelioid vascular neoplasms, one fused to NFATC2 while two others to NFATC1. There were three females and two males, with a wide age range at presentation, mean of 44 years. The lesions occurred in the pelvis, maxillary sinus, and humerus. Two patients presented with polyostotic disease, both located in the pelvic bones. Two patients had available follow-up, one developed two local recurrences in the humerus over a 15-year period, while the other showed no recurrence 4 years subsequent to an en-bloc resection. Tumors were positive for CD31 and ERG, while negative for EMA, CK, synaptophysin, and chromogranin. FISH confirmed this abnormality in all cases, none of them being associated with gene amplifications. Further studies are needed to establish the pathogenetic relationship of this rare molecular subset with other epithelioid vascular tumors and to determine its clinical behavior.

Tea polyphenol alleviate Aeromonas hydrophila - induced intestinal physical barrier damage in grass carp (Ctenopharyngodon idella)

This study aimed to investigate the effects of tea polyphenol (TP) supplementation on attenuating Aeromonas hydrophila - induced intestinal barrier function injury in fish. A total of 540 healthy grass carp (187.49 ± 0.66 g) were randomly divided into six groups with three replicates and fed TP-supplemented diets at 0, 40, 80, 120, 160 and 200 mg/kg for 60 days. After the growth trial, 24 fish per group were randomly selected for a challenge test with A. hydrophila for 6 days. The results indicated that an appropriate level of TP (120 mg/kg diet) repair damaged the intestinal morphology of fish induced by A. hydrophila. Additionally, appropriate level of TP ameliorated the intestinal apical junctional complex partly, which was partly related to the up-regulation of the expressions of tight junction and adherent junction proteins via the RhoA/ROCK pathway in the fish intestine. Based on the results of this research, dietary TP supplementation possesses a protective function of the intestinal physical barrier in fish against A. hydrophila, making TP a functional feed additive for aquaculture and providing a solution for the issue of hazards to human health caused by antibiotic residues in aquatic food.

Effects of Harvest, Natural Mortality, and Escapement on Reservoir Walleye Populations

AbstractWalleye Sander vitreus are commonly introduced to reservoirs and provide valued fisheries. Walleye are lost though harvest and natural mortality in all systems, but escapement may also reduce reservoir populations. However, the effects of harvest, natural mortality, and escapement loss on reservoir Walleye populations are not known. Our objective was to quantify Walleye harvest, natural mortality, and escapement in two Iowa reservoirs (Big Creek Lake and Brushy Creek Lake) to understand how these factors limit populations. We also assessed Walleye behaviors and compared them among escaped, harvested, and in‐lake Walleye to determine if behavior was associated with fate. Walleye were radio‐tagged beginning in October 2016 and tracked through May 2019. Telemetry was used to estimate annual core and home ranges, seasonal depth use, and movement rates. Detection histories were analyzed using a multistate capture–recapture model with environmental covariates to estimate weekly harvest, natural mortality, and escapement. Harvest was greater in Big Creek than Brushy Creek and was higher in April through July compared to other months. Natural mortality was positively related to water temperature but did not differ between systems. No Walleye escaped from Big Creek (fish barrier on spillway), but escapement at Brushy Creek (no fish barrier) was positively related to mean water levels during April. During 2017–2018, annual Walleye escapement ranged from 22% to 47% at Brushy Creek (0% at Big Creek), harvest ranged from 13% to 27%, and natural mortality ranged from 36% to 38%. Depth of habitat occupied by Walleye was shallower during spring and summer when escapement occurred, intermediate in fall, and deepest during winter. Escaped Walleye at Brushy Creek used greater depths and moved less than in‐lake Walleye; however, other behaviors did not differ among Walleye groups. Our results suggest that escapement can have a larger effect than harvest on reservoir Walleye populations in systems without physical barriers, and it should be taken into consideration when managing reservoir Walleye fisheries.

Analysis of TNF alpha and Interlukin-1β genes in Oreochromis niloticus: inflammatory responses induced by Myxobolus spp. and Trichodina spp.

The cultured and wild specimens of the Nile tilapia ( Oreochromis niloticus ) are often infected by different hazardous as helminths; protozoa and arthropod which cause various degrees of diseases in such fish. The aim of this study was to record the most common protozoan parasites in the Nile tilapia in Egypt, and also assessment of the immunological changes through analyzing two genes (Tumor Necrosis Factor alpha, TNF-α; and Interlukin-1β, IL- 1β) in the infected fishes using qRT-PCR. Therefore, each fish individual was examined carefully, and smears were prepared from each organ; stained with Giemsa dye and examined under a light microscope. qRT-PCR was performed on infected tissues (skin and gills) by various collected parasites. Four trichodinid species ( Trichodinella heterodentata , T. centrostrigeata , T. epizootica , Paratrichodina Africana ,) were isolated and identified; also two Myxobolus spp. ( M. tilapiae and M. heterosporous ) were fully described. In skin, TNF-α in M. tilapiae and mixed groups were nearly similar and were significantly higher than Trichodina spp. group. IL-1β of M. tilapiae group was significantly lower than that of the mixed group; Trichodina spp. and control groups. In gills, TNF-α of the mixed group showed the significantly highest value. IL-1β was nearly same in all groups. We conclude that the skin is nearly higher in upregulation of the two studied genes comparing to the gills analysis, since it is considered as the first barrier in fish and contains many immunological defined cells.

Statistical Evaluation of Behavior and Population Dynamics Models Predicting Movement and Proportional Entrainment Loss of Adult Delta Smelt in the Sacramento–San Joaquin River Delta

There has been considerable debate about effects of entrainment of endangered Delta Smelt (Hypomesus transpacificus) at water export facilities located in the Sacramento–San Joaquin River Delta. In this paper we use a behavior-driven movement model (BMM) to simulate the movement of adult Delta Smelt, which, in conjunction with a population dynamics model, estimates the proportion of the population that is lost to entrainment, i.e., proportional entrainment loss (PEL). Parameters of the population model are estimated by maximum likelihood by comparing predictions to data from Fall Midwater Trawl (FMWT) and Spring Kodiak Trawl (SKT) surveys, as well as to daily salvage estimates. Our objectives are to evaluate different movement behavior hypotheses, to rank estimates of PEL based on how well predictions fit the data, and to sharpen our understanding of the data to inform future research and monitoring decisions. We applied the modeling framework to data from water year 2002—a year when salvage was high—and tested 30 combinations of six behavior and five population dynamics models. More complex process and observation assumptions in the population model led to much improved fits in most cases, but did not appreciably influence PEL predictions, which were largely determined by movement predictions from the BMMs. Estimates of PEL varied considerably among behaviors (2% to 40%). The model with the highest predictive capability explained 98% of the variation in FMWT data across regions, 70% of the variation in SKT data across regions and surveys, and 28% and 43% of the daily variation in salvage at federal and state fish screening facilities, respectively. The PEL estimate from this model was 35%, more than double the original estimate from Kimmerer (2008) of 15%. While PEL estimates provided in this study should be considered preliminary, our framework for testing combined behavior-driven movement models and population dynamics models is an improvement compared to earlier efforts.

Statistical Evaluation of Behavior and Population Dynamics Models Predicting Movement and Proportional Entrainment Loss of Adult Delta Smelt in the Sacramento–San Joaquin River Delta

There has been considerable debate about effects of entrainment of endangered Delta Smelt (Hypomesus transpacificus) at water export facilities located in the Sacramento–San Joaquin River Delta. In this paper we use a behavior-driven movement model (BMM) to simulate the movement of adult Delta Smelt, which, in conjunction with a population dynamics model, estimates the proportion of the population that is lost to entrainment, i.e., proportional entrainment loss (PEL). Parameters of the population model are estimated by maximum likelihood by comparing predictions to data from Fall Midwater Trawl (FMWT) and Spring Kodiak Trawl (SKT) surveys, as well as to daily salvage estimates. Our objectives are to evaluate different movement behavior hypotheses, to rank estimates of PEL based on how well predictions fit the data, and to sharpen our understanding of the data to inform future research and monitoring decisions. We applied the modeling framework to data from water year 2002—a year when salvage was high—and tested 30 combinations of six behavior and five population dynamics models. More complex process and observation assumptions in the population model led to much improved fits in most cases, but did not appreciably influence PEL predictions, which were largely determined by movement predictions from the BMMs. Estimates of PEL varied considerably among behaviors (2% to 40%). The model with the highest predictive capability explained 98% of the variation in FMWT data across regions, 70% of the variation in SKT data across regions and surveys, and 28% and 43% of the daily variation in salvage at federal and state fish screening facilities, respectively. The PEL estimate from this model was 35%, more than double the original estimate from Kimmerer (2008) of 15%. While PEL estimates provided in this study should be considered preliminary, our framework for testing combined behavior-driven movement models and population dynamics models is an improvement compared to earlier efforts.

Acoustic and Light Selective Behavioral Guidance Systems for Freshwater Fish

The use of non-physical barriers, particularly based on acoustic and luminous stimuli has been historically used to influence the behavior of fish, mainly for fishing purposes. Nowadays, behavioral barriers and guidance systems have been developed, not only to deter movements of fish, but also to promote behavioral responses with the objective of native fish protection, in particular the potamodromous species, reducing their mortality in the hydraulic structures of dams and guiding them towards transposition systems or to replacement habitats in regularized water bodies. This review details the use of acoustic and luminous systems and their evolution in recent years (Scopus 2012–2019) for the development of selective behavioral barriers for fish. We found that recent technologies try to identify new acoustic and luminous sensory ranges. Ambient sound, sound of predators or luminous spectral bands with different wavelengths have been used to selectively stimulate target and non-target species, in order to improve the effectiveness of repulsive/attractive systems for fish. Guidelines for future research in the area are also present.

Leaky barriers: leaky enough for fish to pass?

Perceived as environmental-friendly hydraulic structures, leaky barriers used for natural flood management are introduced into rivers, potentially creating migration barriers for fish. Using sustainable, local materials to construct wooden barriers across river channels in upper catchments, these barriers aim to slow down the flow, reduce flood peaks and attenuate the flow reaching downstream communities. Yet little is known about their impact on hydrodynamics and fish passage. Here, we examined two model barrier designs under 100% and 80% bankfull flow conditions in an open channel flume. These barriers included a porous and a non-porous design, with the latter emulating the natural accumulation of brush, sediment and leaf material between logs over time. Flow visualization and velocity measurements recorded with acoustic Doppler velocimetry characterized the flow field upstream and downstream of the barriers. Our fish behavioural studies revealed that juvenile salmon (Salmo salar) movement between downstream and upstream sections of the flume was inhibited by barrier design rather than discharge, influencing upstream fish passage and their spatial preference, indicating the importance of barrier design criteria to facilitate fish movement.

Evaluating a Permeable‐Style Fish Barrier to Prevent the Upstream Recolonization of Nonnative Trout during an Eradication Project

AbstractIn the western United States, the introduction of nonnative Brook Trout Salvelinus fontinalis has had deleterious effects on native Cutthroat Trout Oncorhynchus clarkii subspecies, and often their populations must be controlled or removed if Cutthroat Trout are to persist. Man‐made fish migration barriers are integral components of stream restoration projects, and typical designs are intended to be permanent and to funnel water over a drop and onto a splash pad. The water elevation drop and the splash pad, which prevents a jumping pool, are mechanisms intended to prevent fish from navigating upstream past the structure. In this study, we installed a temporary, permeable‐style barrier that was designed to have water flow onto and through a horizontal, expanded steel panel. When fish attempted to move upstream, they would follow the water flow and end up underneath the barrier, with no opportunity to move further. The permeable barrier proved effective in preventing the upstream movement of Brook Trout, and additional advantages to this barrier style included straightforward permitting, low cost, ease of installation, and quick removal. The main disadvantage was the periodic cleaning (average of 7 trips/year) that was required to maintain its intended function. The permeable barrier separated stream reaches for 5 years, allowing biologists to (1) eradicate Brook Trout upstream through multiple‐pass backpack electrofishing while preserving native Yellowstone Cutthroat Trout O. clarkii bouvieri and (2) apply a successful piscicide treatment below the barrier.

Nutrient Digestibility, Growth, Mucosal Barrier Status, and Activity of Leucocytes From Head Kidney of Atlantic Salmon Fed Marine- or Plant-Derived Protein and Lipid Sources.

Nutrient digestibility, growth, and mucosal barrier status of fish skin, gills, and distal intestine were studied in Atlantic salmon fed feeds based on marine or plant-derived ingredients. The barrier status was assessed by considering the expression of four mucin genes, five genes that encode antimicrobial proteins, distal intestine micromorphology, and design-based stereology of the midgut epithelium. In addition, the head kidney leukocytes were examined using flow cytometry; to understand the differences in their counts and function. Five experimental feeds containing the main components i) fishmeal and fish oil (BG1), ii) soybean meal (BG2; to induce enteritis), iii) fishmeal as the main protein source and rapeseed oil as the main lipid source (BG3), iv) a mix of plant protein concentrates as the protein sources and fish oil as the lipid source (BG4), and v) plant and marine ingredients in the ratio 70:30 (BG5) were produced for the study. Atlantic salmon with initial weight 72.7 ± 1.2 g was offered the experimental feeds for 65 days. The results revealed that the weights of all fish groups doubled, except for fish fed BG2. Fish fed the BG2 diet had lower blood cholesterol concentration, developed enteritis, had lower expression of muc2 in the distal intestine, and had a compromised barrier status in the intestine. Expression of both the mucin genes and genes that encode antimicrobial peptides were tissue-specific and some were significantly affected by diet. The fish fed BG1 and BG3 had more head kidney lymphocyte-like cells compared to BG5-fed fish, and the phagocytic activity of macrophage-like cells from the head kidney was the highest in fish fed BG1. The intestinal micromorphology and the mucosal mapping suggest two different ways by which plant-based diets can alter the gut barrier status; by either reducing the mucous cell sizes, volumetric densities and barrier status (as noted for BG2) or increasing volumetric density of mucous cells (as observed for BG4 and BG5). The results of the compromised intestinal barrier in fish fed plant ingredients should be further confirmed through transcriptomic and immunohistochemical studies to refine ingredient composition for sustainable and acceptable healthy diets.

Bubble barriers to guide downstream migrating Atlantic salmon (Salmo salar): An evaluation using acoustic telemetry

Structures for guiding fish around migration barriers are frequently used for maintaining connectivity in regulated riverine systems. However, for non-physical barriers, experimental studies providing direct and detailed observations of fish–barrier interactions in rivers are largely lacking. In this study, we quantify the efficiency of bubble barriers (alone or in combination with light stimuli, and in both daylight and darkness) for diverting downstream migrating Atlantic salmon (Salmo salar). Both a laboratory-based migration experiment and a large-scale field experiment in a regulated river were used to evaluate efficiency of bubble barriers. In the latter, we used acoustic telemetry to provide in situ measurements of how downstream migrating Atlantic salmon smolts interact with bubble barriers. We show that bubbles divert smolts with high efficiency in both a laboratory flume (95%) and in natural settings (90%). This latter efficiency is higher compared to an already present physical barrier (46%) covering the upper two meters of the water column in the large river. The bubble barrier did not affect flume migration in darkness, suggesting that visual cues are crucial for the observed repelling effect of bubbles. We conclude that bubble barriers can be effective, largely maintenance free and low-cost alternatives to physical structures currently used to divert salmon away from high-mortality passages.

Distribution of freshwater fish from the Southern Neotropics reveals three new areas of endemism and show diffuse limits among freshwater ecoregions

Abstract Ecoregions and areas of endemism are central concepts in biogeography. Based on collection records and the Endemic Analyses implemented with NDM/VNDM method we analyzed fish areas of endemism in the junction of three freshwater ecoregions related to the Rio de la Plata estuary (Lower Parana, Lower Uruguay, Laguna dos Patos) in Southern Neotropical region. Using two grid cell sizes, results obtained showed the same general patterns. Areas of endemism recovered were mainly associated either to Lower Uruguay or to Laguna dos Patos. In both ecoregions nested areas of endemism were identified within larger patterns of endemism. Noteworthy, one area recovered occurred across Lower Uruguay and Laguna dos Patos limits. Our results also suggest a revision of the Lower Uruguay and Lower Parana ecoregion limits, and highlight the relevance of the Rio de la Plata estuary as a barrier and corridor for freshwater fishes in the area.

Length-Weight Relationships of 12 Fish Species from the Köyceğiz Lagoon, Turkey

This study provides the length-weight relationships of 12 fish species that belong to ten families from the Köyceğiz Lagoon, Turkey; Dicentrarchus labrax (Linnaeus, 1758); Diplodus annularis (Linnaeus, 1758); Diplodus sargus (Linnaeus, 1758); Dussumieria elopsoides Bleeker, 1849; Engraulis encrasicolus (Linnaeus, 1758); Oreochromis niloticus (Linnaeus, 1758); Gobius niger Linnaeus, 1758; Mullus barbatus barbatus Linnaeus, 1758; Sparus aurata Linnaeus, 1758; Siganus rivulatus Forsskål & Niebuhr, 1775; Solea solea (Linnaeus, 1758); Trachinotus ovatus (Linnaeus, 1758). A total of 720 fish samples were collected with fish barrier, trammel net, beach seine and cast-net. The growth type of D. annularis (b=3.148), D. elopsoides (b=3.089), G. niger (b=3.154), S. solea (b=3.124) was determined as positive allometry and E. encrasicolus (b=2.814), D. labrax (b=2.764), T. ovatus (b=2.901) was determined as negative allometry whereas D. sargus (b=2.995), M. barbatus barbatus (b=3.003), O. niloticus (b=3.088), S. aurata (b=3.009) and S. rivulatus (b=3.079) showed isometry. The results of this investigation will contribute to further fishery studies in the Köyceğiz Lagoon.

Fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations.

SummaryWhole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet.

Population effect of a large‐scale stream restoration effort on Chinook salmon in the Pahsimeroi River, Idaho

AbstractStream habitat restoration is an important tool for fisheries management in impaired lotic systems. Although small‐scale benefits of stream habitat restoration are commonly investigated, it is difficult to demonstrate population effects. The Pahsimeroi River Chinook salmon Oncorhynchus tshawytscha population was previously restricted to the lower portion of the river by multiple irrigation structures. To address fish passage issues, a combination of restoration projects was initiated including barrier removals, instream flow enhancements and installation of fish screens on diversions. The largest barrier was removed in 2009, more than doubling the amount of accessible linear habitat. We hypothesized restoration efforts would expand the distribution of spawning salmon in the Pahsimeroi River watershed, leading to a broader distribution of juveniles. We also hypothesized a broader juvenile distribution would have population effects by reducing the prevalence of density‐dependent growth and survival. Redds were documented in newly accessible habitat immediately following barrier removal and accounted for a median of 42% of all redds in the Pahsimeroi River watershed during 2009–2015. Snorkel surveys also documented juvenile rearing in newly accessible habitat. Juvenile productivity increased from a median of 64 smolts/female spawner for brood years 2002–2008 to 99 smolts/female spawner for brood years 2009–2014. Overall, results suggested increased habitat accessibility in the Pahsimeroi River broadened the distribution of spawning adult and rearing juvenile salmon and reduced the effects of density‐dependent survival. Large‐scale stream restoration efforts can have a population effect. Despite the large‐scale effort and response, habitat restoration alone is likely not sufficient to restore this population.

Research Progress on the Polymeric Immunoglobulin Receptor (pIgR) in Fish

There are a large number of pathogens in the water where fish live, and the mucosal-associated lymphoid tissues (MALTs), such as skin, gill and intestine, are the first contact parts when pathogens infect fish. The secreted mucus of these tissues constitutes the first barrier for fish against the invasion of external pathogens. Mucosal immunity can identify and neutralize pathogens and induces immunocytes to devour pathogens and the like. As a key factor in the mucosal immune system, the polymeric immunoglobulin receptor (pIgR) is capable of mediating the transport and secretion of polymeric immunoglobulins towards mucus. The effective secretion of the pIgR is necessary for polymeric immunoglobulins (pIg) to exert mucosal defence and plays a significant role in fish immunity. With the deepening of research into fish immunoglobulins, the pIgR has become a research hotspot. The molecular structure, genetic structure and expression pattern of the pIgR and the important role it plays in mucosal immunity were summarized in this study, which contributed to a deeper understanding of fish mucosal immunity and laid a foundation for further exploration of the action mechanism and functions of the pIgR in fish.

Isolation, characterization and performance of extra cellular polymer substances (EPS) producing bacteria from biofloc culture water of Nile tilapia using distillery spentwash as carbon source

The present study aimed to isolate and characterize the Extracellular polymeric substance (EPS) producing bacteria from biofloc reared Nile tilapia (Chitralada) ponds. Distillery spentwash was used as a carbon source to maintain the C: N ratio at 10: 1 in the fish culture ponds and screening of bacteria were done fortnightly in 180 days culture. Out of 38 bacterial isolates, 7 isolates were found to produce EPS. Based on 16s rRNA sequence analysis the isolates were identified as Bacillus subtilis, B. megaterium, B. infantis, B. cereus, Pseudomonas balearica, P. mendocina and P. alcaligenes. The highest production of EPS was recorded in B. cereus (1.25 g/L). EPS extracted from Bacillus cereus was reported to have higher protein (89 μg/ml) and B. subtilis possessed higher carbohydrate (753.75 μg/ml). Maximum flocculating ability of 40.18% in B. cereus and higher emulsifying activity of 63.53% was observed in B. megaterium. The EPS extracted from B. infantis showed lower sludge volume index on its treatment with aquaculture sludge (15.38 ml/g). Absorption band in the range of 4,000/cm to 450/cm using FTIR analysis confirmed the presence of characteristic functional bands arising from polysaccharides, nucleic acids and proteins. The results indicated the presence of EPS producing bacteria in biofloc based Nile tilapia aquaculture systems.

Hybrid modelling of low velocity zones in box culverts to assist fish passage: Why simple is better!

AbstractA culvert is a covered road structure constructed to pass flood and drainage. The engineering design principle of culverts focuses on optimising flood capacity at the lowest possible cost, resulting in high flow velocity through the barrel. With modern engineering design being more environmentally aware, culverts are considered common barriers for fish migrating upstream due to the excessive barrel velocity. The migration of fish upriver is important for their breeding and feeding activities, contributing to a stable population and species diversity. Improved or novel design for a fish‐friendly culvert is needed to ensure well‐being of local fish community. This article is a review of recent developments in seeking a solution for a better fish‐friendly culvert design. A major common feature of the reviewed studies is the application of hybrid modelling, combining laboratory experiments and numerical Computational Fluid Dynamics (CFD) modelling together. Various design alternatives were compared for pros and cons: channel roughening, installation of speed‐reducing structures (e.g., baffles or beams), and simply widening the channel by adding more culvert units (boxes). Overall, channel widening stands to be a better design choice due to its suitability for both flood passage and fish passage, with little impact on operation safety and a reduced maintenance cost.

Development of Carbon Dioxide Barriers to Deter Invasive Fishes: Insights and Lessons Learned from Bigheaded Carp

Invasive species are a threat to biodiversity in freshwater. Removing an aquatic invasive species following arrival is almost impossible, and preventing introduction is a more viable management option. Bigheaded carp are an invasive fish spreading throughout the Midwestern United States and are threatening to enter the Great Lakes. This review outlines the development of carbon dioxide gas (CO2) as a non-physical barrier that can be used to deter the movement of fish and prevent further spread. Carbon dioxide gas could be used as a deterrent either to cause avoidance (i.e., fish swim away from zones of high CO2), or by inducing equilibrium loss due to the anesthetic properties of CO2 (i.e., tolerance). The development of CO2 as a fish deterrent started with controlled laboratory experiments demonstrating stress and avoidance, and then progressed to larger field applications demonstrating avoidance at scales that approach real-world scenarios. In addition, factors that influence the effectiveness of CO2 as a fish barrier are discussed, outlining conditions that could make CO2 less effective in the field; these factors that influence efficacy would be of interest to managers using CO2 to target other fish species, or those using other non-physical barriers for fish.

Abstract 3641: Successful classification of hematological neoplasm by array profile

Abstract In addition to structural chromosome aberrations resulting in fusion genes, the genome profile of haematological malignancies is characterized by copy number changes (gains and losses) relative to the ploidy level. Array comparative genome hybridization (aCGH)1 Combined with FISH and/or multiplex PCR array screening offers a reliable tool for assessment of genome complexity in haematological malignancies in diagnostic settings. The aCGH assay in our diagnostic algorithm uses 8 × 60K SurePrint G3 (Agilent, USA). The slides are scanned to measure the fluorescence ratio (FR), software evaluates imbalances. We recognize that the raw data in the form of log ratios, some 64,000 data points, contain sufficient information to identify the disease category without resorting to converting the log ratios to gains and losses and mapping them to individual chromosomes, a process open to operator interpretation. As an alternative and bearing in mind the current interest in machine learning, we attempted to auto-classify the data for the modest collection of 2,300 patient samples in our archive, according to their WHO classification. We were able to collect 175 samples for each group classified as myelodisplasia (MDS), acute myeloid leukemia (AML), myeloma (MM) and chronic lymphocytic leukemia (CLL), We used a Logistic Regression Classifier implemented in Mathematica 12. The classifier took only 2 minutes on average to complete the training. We took a total of 700 array sample files, each of 59,032 data points, of which 100 were randomly selected as a validation set. The balance of 600 files, distributed evenly and randomly over the 4 test diseases were used as a training set. We used a Confusion Matrix to evaluate and display the results as shown in the table. Confusion MatrixAMLCLLMDSMMTotalAML1609025CLL0150116MDS0116017MM1021417Predicted17162715 In spite of the small training set we correctly classified the MDS (16/17), CLL (15/16) and MM (14/17), 9 AML were reported as MDS a due to sharing genome imbalances. There was also confusion between the B cell disorders, MM and CLL known to carry overlapping genome aberrations. The auto classification offered by this method is a promising attempt to support a speedy and reliable assessment of genome complexity. There is no doubt that a better classifier would have been created with a larger training set. 1 Kallioniemi A et al., Kallioniemi OP, Sudar DA, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992). “Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors”. Science. 258 (5083): 818-821). Citation Format: Colin Grace, Temenuzhka Boneva, Elisabeth P. Nacheva. Successful classification of hematological neoplasm by array profile [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3641.