Fifteen years of quantitative trait loci studies in fish: challenges and future directions

Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine‐mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage‐based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype–phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future.     

Factors affecting the within-river spawning migration of Atlantic salmon,with emphasis on human impacts

We review factors affecting the within-river spawning migration of Atlantic salmon. With populations declining across the entire distribution range, it is important that spawners survive in the last phase of the spawning migration. Knowledge on the factors affecting migration is essential for the protection of populations, and to increase the success of reintroduction programmes. A number of studies have documented that the upstream migration may be delayed for many weeks at man-made obstacles such as power station outlets, residual flow stretches, dams, weirs and fishways. The fish may also be delayed at natural migration barriers. Often, the magnitude of delay is not predictable; fish may be considerably delayed at barriers that appear to humans to be easily passable, or they may quickly pass barriers that appear difficult. Stressful events like catch-and-release angling may affect upstream migration. Impacts of human activities may also cause altered migration patterns, affect the within-river distribution of the spawning population, and severe barriers may result in displacement of the spawning population to other rivers. Factors documented to affect within-river migration include previous experience, water discharge, water temperature, water velocity, required jump heights, fish size, fish acclimatisation, light, water quality/pollution, time of the season, and catch and handling stress. How each of these factors affects the upstream migration is to a varying extent understood; however, the effects may differ among different river sections and sites. There are likely a number of additional important factors, and the relationship between different factors is complex. The understanding of general mechanisms stimulating fish within-river migration are still lacking, and it cannot be reliably predicted under which conditions a fish will pass a given migration barrier or which conditions are needed to stimulate migration at different sites. The strong focus on the effects of water discharge in past work may have hampered consideration of other factors. Exploration of the influence of these other factors in future studies could improve our understanding of what controls the upstream migration.     

Factors influencing the survival of outmigrating juvenile salmonids through multiple dam passages: an individual‐based approach

Substantial declines of Pacific salmon populations have occurred over the past several decades related to large‐scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia River Basin, migrating juvenile salmonids may pass as many as eight large‐scale hydropower projects before reaching the ocean; however, the cumulative effects of multiple dam passages are largely unknown. Using acoustic transmitters and an extensive system of hydrophone arrays in the Lower Columbia River, we calculated the survival of yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) passing one, two, or three dams. We applied a unique index of biological characteristics and environmental exposures, experienced by each fish individually as it migrated downstream, in order to examine which factors most influence salmonid survival. High outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity, and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to a press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids at this life stage.     

Chirality of organophosphorus pesticides: Analysis and toxicity

Although the importance of chirality in organophosphorus compounds (OPs) is well recognized in relation to their biological effects, as with most chiral pesticides, OPs are generally marketed, used and released to the environment as racemates (i.e., equimolar mixtures of enantiomers). In addition, research on enantioselective environmental fate and effects of chiral OPs is still limited, particularly in the evaluation of enantioselectivity in their environmental degradation. A large number of OPs are chiral compounds, and yet enantioselectivity in their environmental fate and effects is rarely addressed. This paper highlights the current state of knowledge on the environmental occurrence and behavior of chiral OP pesticides. Developments in enantioselective analytical techniques, specifically gas chromatography (GC), high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE), as applied in the evaluation of enantiomer-specific fate and effects of chiral OPs, are also discussed.     

Energetic and biomechanical constraints on animal migration distance

Animal migration is one of the great wonders of nature, but the factors that determine how far migrants travel remain poorly understood. We present a new quantitative model of animal migration and use it to describe the maximum migration distance of walking, swimming and flying migrants. The model combines biomechanics and metabolic scaling to show how maximum migration distance is constrained by body size for each mode of travel. The model also indicates that the number of body lengths travelled by walking and swimming migrants should be approximately invariant of body size. Data from over 200 species of migratory birds, mammals, fish, and invertebrates support the central conclusion of the model - that body size drives variation in maximum migration distance among species through its effects on metabolism and the cost of locomotion. The model provides a new tool to enhance general understanding of the ecology and evolution of migration.     

Analytical methodologies for the detection and structural characterization of phosphorylated proteins

Phosphorylation of proteins is a frequent post-translational modification affecting a great number of fundamental cellular functions in living organisms. Because of its key role in many biological processes, much effort has been spent over the time on the development of analytical methodologies for characterizing phosphoproteins. In the past decade, mass spectrometry-based techniques have emerged as a viable alternative to more traditional methods of phosphorylation analysis, providing accurate information for a purified protein on the number of the occurring phosphate groups and their exact localization on the polypeptide sequence. This review summarizes the analytical methodologies currently available for the analysis of protein phosphorylation, emphasizing novel mass spectrometry (MS) technologies and dedicated biochemical procedures that have been recently introduced in this field. A formidable armamentarium is now available for selective enrichment, exaustive structural characterization and quantitative determination of the modification degree for phosphopeptides/phosphoproteins. These methodologies are now successfully applied to the global analysis of cellular proteome repertoire according a holistic approach, allowing the quantitative study of phosphoproteomes on a dynamic time-course basis. The enormous complexity of the protein phosphorylation pattern inside the cell and its dynamic modification will grant important challenges to future scientists, contributing significantly to deeper insights into cellular processes and cell regulation.     

Imaging stem cell implant for cellular-based therapies

Stem cell-based cellular therapy represents a promising outlook for regenerative medicine. Imaging techniques provide a means for noninvasive, repeated, and quantitative tracking of stem cell implant or transplant. From initial deposition to the survival, migration and differentiation of the transplant/implanted stem cells, imaging allows monitoring of the infused cells in the same live object over time. The current review briefly summarizes and compares existing imaging methods for cell labeling and imaging in animal models. Several studies performed by our group using different imaging techniques are described, with further discussion on the issues with these current imaging approaches and potential directions for future development in stem cell imaging.     

A Macrophyte-Based Rapid Biosurvey of Stream Water Quality: Restoration at the Watershed Scale

The restoration of chemically degraded rivers, lakes, and estuaries with large watersheds and pollution sources that are primarily diffuse in nature requires the grading of thousands of kilometers of tributary streams. Many population-and community-oriented biomonitoring methods have been developed that avoid the cost limitations of chemical/biomarker/bioassay approaches and the serious limitations of single-factor analysis as related to complex systems. In this study of the coastal plain and piedmont geomorphologic provinces of the Chesapeake Bay watershed, we have demonstrated a set of quantitative measures based on analysis of macrophyte populations that provide statistically significant separation of streams in accordance with their state-issued water quality rating. Macrophytes can be abundant and diverse in lower-order streams, and they demonstrate patterns of community structure and diversity similar to those of other organisms developed for biomonitoring of stream degradation. Unlike organisms previously and extensively used in biomonitoring techniques, however, macrophytes are considerably easier to identify and quantify. In addition, macrophyte techniques provide a range of measures of increasing sensitivity from species numbers at a few sites, to the presence/absence and abundance of indicator species, and, finally, to a diversity analysis based on easily identified species at an extended number of sites. We suggest that the ease of utilization of this methodology will allow repeated surveys of all streams in large watersheds with the invertebrate, fish and diatom biomonitoring to biomarking and chemical bioassays and finally analytical chemistry, progressively applied to verify and then identify specific pollution sources (“hot spots”) in a more limited number of problem streams.     

Experimental effect of alloocimene on soft tissue wound

The action of alloocymen--a representative of carotinoid polyens--metabolism stimulants, active drugs normalising the trophic process, on wound healing by secondary tension of soft tissue was studied. Alloocymen increased the intensity of healing of skin and skin-muscle wounds, accelerated in a number of cases complete wound healing, produced an ntiinflammatory action on the wound and the adjacent zones, eliminated or limited edema, hypermia, maceration, hemorrage, prevented the development of acute inflammation. The applied methods of quantitative analysis of these alloocymen effects make possible evaluation of it's positive actions on trophic process in the course of wound healing.     

Fluorescence nanoscopy. Methods and applications

Fluorescence nanoscopy refers to the experimental techniques and analytical methods used for fluorescence imaging at a resolution higher than conventional, diffraction-limited, microscopy. This review explains the concepts behind fluorescence nanoscopy and focuses on the latest and promising developments in acquisition techniques, labelling strategies to obtain highly detailed super-resolved images and in the quantitative methods to extract meaningful information from them.     

Methods Used to Assess Non-target Effects of Invertebrate Biological Control Agents of Arthropod Pests

The number of concerns regarding potential non-target effects of invertebrate biological control agents of arthropods has risen over the last decade and an increasing number of studies have since dealt with this topic. Despite some recent international initiatives aimed at providing guidance for risk assessment of biological control agents, detailed methods on how tests should be designed and conducted to assess for potential non-target effects still need to be provided. It is believed that this review comes at an ideal time, giving an overview of methods currently applied in the study of non-target effects in biological control of arthropod pests. It provides the first step towards the ultimate goal of devising guidelines for the appropriate methods that should be universally applied for the assessment and minimisation of potential non-target effects. The main topics that are reviewed here include host specificity (including field surveys, selection of non-target test species and testing protocols), post-release studies, competition, overwintering and dispersal. Finally, a number of conclusions that have emerged from this comprehensive compilation of studies are drawn, addressing potential non-target effects in arthropod biological control.     

Principles and limitations of computational microRNA gene and target finding

In 2001 there were four PubMed entries matching the word "microRNA" (miRNA). Interestingly, this number has now far exceeded 1300 and is still rapidly increasing. This more than anything demonstrates the extreme attention this field has had within a short period of time. With the large amounts of sequence data being generated, the need for analysis by computational approaches is obvious. Here, we review the general principles used in computational gene and target finding, and discuss the strengths and weaknesses of the methods. Several methods rely on detection of evolutionary conserved candidates, but recent methods have challenged this paradigm by simultaneously searching for the gene and the corresponding target(s). Whereas the early methods made predictions based on sets of hand-derived rules from precursor-miRNA structure or observed target-miRNA interactions, recent methods apply machine learning techniques. Even though these methods are already powerful, the amount of data they rely on is still limited. Since it is evident that data are continuously being generated, it must be anticipated that these methods will further improve their performance.     

Mathematical modelling of the mitochondrial apoptosis pathway

Mitochondria are pivotal for cellular bioenergetics, but are also a core component of the cell death machinery. Hypothesis-driven research approaches have greatly advanced our understanding of the role of mitochondria in cell death and cell survival, but traditionally focus on a single gene or specific signalling pathway at a time. Predictions originating from these approaches become limited when signalling pathways show increased complexity and invariably include redundancies, feedback loops, anisotropies or compartmentalisation. By introducing methods from theoretical chemistry, control theory, and biophysics, computational models have provided new quantitative insights into cell decision processes and have led to an increased understanding of the key regulatory principles of apoptosis. In this review, we describe the currently applied modelling approaches, discuss the suitability of different modelling techniques, and evaluate their contribution to the understanding of the mitochondrial apoptosis pathway. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.     

Measuring cortisol,the major stress hormone in fishes

Stress in teleosts is an increasingly studied topic because of its interaction with growth, reproduction, immune system and ultimately fitness of the animal. Whether it is for evaluating welfare in aquaculture, adaptive capacities in fish ecology, or to investigate effects of human-induced rapid environmental change, new experimental methods to describe stress physiology in captive or wild fish have flourished. Cortisol has proven to be a reliable indicator of stress and is considered the major stress hormone. Initially principally measured in blood, cortisol measurement methods are now evolving towards lower invasiveness and to allow repeated measurements over time. We present an overview of recent achievements in the field of cortisol measurement in fishes, discussing new alternatives to blood, whole body and eggs as matrices for cortisol measurement, notably mucus, faeces, water, scales and fins. In parallel, new analytical tools are being developed to increase specificity, sensitivity and automation of the measure. The review provides the founding principles of these techniques and introduces their potential as continuous monitoring tools. Finally, we consider promising avenues of research that could be prioritised in the field of stress physiology of fishes.     

我国过鱼设施建设需求、成果及存在的问题

本文首先阐述了水利水电工程对河流连通性的影响以及修建过鱼设施的对策,然后从河流破碎化程度和鱼类洄游习性的角度分析了国内建设过鱼设施的需求,介绍了国内建设过鱼设施的成果,最后提出了6点过鱼设施相关问题和建议:(1)利用多指标量化评价的方法,科学地确定过鱼对象;(2)以复杂流场为背景条件,贴合实际地推进鱼类上溯行为研究;(3)对过鱼设施加大资金投入,扩大设施规模,加大过鱼设施过水流量(至少应为河流流量的1%);(4)为鱼类下行、低水头水工建筑物引起的跌水河段建设过鱼设施;(5)扩大过鱼效果评估的覆盖面,提高监测时长和频率,提出有广泛适用性的监测评估方法;(6)栖息地修复、增殖放流、生态调度、分层取水等多手段联动,确保鱼类通过过鱼设施后仍然能够生存。     

Accounting for Limited Detection Efficiency and Localization Precision in Cluster Analysis in Single Molecule Localization Microscopy

Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization.     

Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta

Populations of juvenile salmon emigrating from natal rivers to the ocean must often traverse different migratory pathways that may influence survival. In regulated rivers, migration routes may consist of a network of channels such as in the Sacramento-San Joaquin River Delta, or of different passage structures at hydroelectric dams (e.g., turbines or spillways). To increase overall survival, management actions in such systems often focus on altering the migration routing of fish to divert them away from low-survival routes and towards high-survival routes. Here, we use a 3-year data set of route-specific survival and movement of juvenile Chinook salmon in the Sacramento-San Joaquin Delta to quantify the sensitivity of survival to changes in migration routing at two major river junctions in the Sacramento River. Our analysis revealed that changes in overall survival in response to migration routing at one river junction depended not only differences in survival among alternative routes, but also on migration routing at the other river junction. Diverting fish away from a low-survival route at the downstream river junction increased population survival by less than expected, given the difference in survival among routes, because part of the population used an alternative migration route at the upstream river junction. We also show that management actions that influence only migration routing will likely increase survival by less than actions that alter both migration routing and route-specific survival. Our analysis provides an analytical framework to help fisheries managers quantify the suite of management actions likely to maximize increases in population level survival.     

Surgical implantation techniques for electronic tags in fish

Intracoelomic implantation of transmitters into fish requires making a surgical incision, incision closure, and other surgery related techniques; however, the tools and techniques used in the surgical process vary widely. We review the available literature and focus on tools and techniques used for conducting surgery on juvenile salmonids because of the large amount of research that is conducted on them. The use of sterilized surgical instruments properly selected for a given size of fish will minimize tissue damage and infection rates, and speed the wound healing of fish implanted with transmitters. For the implantation of transmitters into small fish, the optimal surgical methods include making an incision on the ventral midline along the linea alba (for studies under 1 month), protecting the viscera (by lifting the skin with forceps while creating the incision), and using absorbable monofilament suture with a small-swaged-on swaged-on tapered or reverse-cutting needle. Standardizing the implantation techniques to be used in a study involving particular species and age classes of fish will improve survival and transmitter retention while allowing for comparisons to be made among studies and across multiple years. This review should be useful for researchers working on juvenile salmonids and other sizes and species of fish.     

INVESTIGATING EVOLUTIONARY TRADE‐OFFS IN WILD POPULATIONS OF ATLANTIC SALMON (SALMO SALAR): INCORPORATING DETECTION PROBABILITIES AND INDIVIDUAL HETEROGENEITY

Evolutionary trade‐offs among demographic parameters are important determinants of life‐history evolution. Investigating such trade‐offs under natural conditions has been limited by inappropriate analytical methods that fail to address the bias in demographic estimates that can result when issues of detection (uncertain detection of individual) are ignored. We propose a new statistical approach to quantify evolutionary trade‐offs in wild populations. Our method is based on a state‐space modeling framework that focuses on both the demographic process of interest as well as the observation process. As a case study, we used individual mark–recapture data for stream‐dwelling Atlantic salmon juveniles in the Scorff River (Southern Brittany, France). In freshwater, juveniles face two life‐history choices: migration to the ocean and sexual maturation (for males). Trade‐offs may appear with these life‐history choices and survival, because all are energy dependent. We found a cost of reproduction on survival for fish staying in freshwater and a survival advantage associated with the “decision” to migrate. Our modeling framework opens up promising prospects for the study of evolutionary trade‐offs when some life‐history traits are not, or only partially, observable.     

Searching for consistently reported up- and down-regulated biomarkers in colorectal cancer: a systematic review of proteomic studies

The cumulative lifetime risk for the development of colorectal cancer in the general population is 6 %. In many cases, early detection by fecal occult blood test is limited regarding sensitivity. Therefore, there is an urgent need for improved diagnostic tests in colorectal cancer. The recent development of high-throughput molecular analytic techniques should allow the rapid evaluation of new diagnostic markers. However, researchers are faced with an overwhelming number of potential markers form numerous colorectal cancer protein expression profiling studies. To address the challenge, we have carried out a comprehensive systematic review of colorectal cancer biomarkers from 13 published studies that compared the protein expression profiles of colorectal cancer and normal tissues. A protein ranking system that considers the number of comparisons in agreement, total sample sizes, average fold-change and direction of differential expression was devised. We observed that some proteins were consistently reported by multiple studies as differentially expressed with a statistically significant frequency (P < 0.05) in cancer versus normal tissues comparison. Our systematic review method identified proteins that were consistently reported as differentially expressed. A review of the top four candidates revealed proteins described previously as having diagnostic value as well as novel candidate biomarkers. These candidates should help to develop a panel of biomarkers with sufficient sensitivity and specificity for the diagnosis of colorectal cancer in a clinical setting.