Proteomic analysis of a rat model of depression

Major depression is one of the most disabling disorders, yet the pathogenesis of this mental disorder is poorly understood. The techniques of proteomics provide us with powerful tools, while the animal models of depression enable research that cannot be performed on humans due to practical difficulties or ethical reasons. In this review, we summarize the characteristics of some most commonly applied rat models of depression, and explore what could be done with novel proteomic approaches to offer an insight to the pathogenesis of major depression, biomarker establishment and drug development.     

Proteomic analysis of a rat model of depression

Major depression is one of the most disabling disorders, yet the pathogenesis of this mental disorder is poorly understood. The techniques of proteomics provide us with powerful tools, while the animal models of depression enable research that cannot be performed on humans due to practical difficulties or ethical reasons. In this review, we summarize the characteristics of some most commonly applied rat models of depression, and explore what could be done with novel proteomic approaches to offer an insight to the pathogenesis of major depression, biomarker establishment and drug development.     

Monitoring of tropical freshwater fish resources for sustainable use

Tropical freshwater ecosystems are some of the world's most biodiverse and productive systems where determining what sustainable exploitation of inland fisheries looks like is particularly challenging. One of the greatest obstacles to sustainable management is collecting and using quality data on fish production and yield. The biodiversity and hydro-ecology of these systems often under open-access governance, add to the complexity of managing them. This paper describes an integrated citizen-science, earth observation, environmental DNA and independent survey approach to collecting fish and fisheries data, using the Cambodian Mekong as a case study.     

The new tools revolutionizing Vibrio science

As microbiologists we live in exciting times. A variety of technical and conceptual developments, particularly in the last decade have revolutionized the field of microbiology, redrawing the landscape, and entirely redefining what is possible. Perhaps this paradigm shift is no more apparent than in the study of vibrios. The family Vibrionaceae are almost unique as a group of bacteria to study in microbiology: they are genomically, phylogenetically and functionally diverse yet a distinct group of environmental bacteria encompassing important human and animal pathogens as well as non-pathogenic species such as ecologically critical symbionts. Sensitive to physiochemical stimuli, they are among the fasting replicating bacteria studied, capable of responding almost immediately to favourable environmental conditions such as those afforded by climate warming. Characterized by an unusual double chromosome and frequently carrying numerous cryptic plasmids – their genomes are often pockmarked with insertion elements, transposons, prophages and integrases – paying testament to past genomic promiscuity. With a strong affinity for environmental niches in freshwater and marine systems, they are among the most numerous bacteria present in our oceans, coasts and freshwater environments. As such they offer something for almost anyone interested in microbiology and represent an excellent example of field of microbiology that has benefitted hugely by advances across a gamut of disciplines – not just microbiological – but encompassing genomics, genetics, oceanography, ecological, earth observations sciences and data visualization, among others. We will briefly outline some of the most exciting, innovative and translational scientific advances that are currently being applied to these ecologically, environmentally and clinically important bacteria.     

Sharing the water column: physiological mechanisms underlying species-specific habitat use in tunas

Tuna species support some of the world’s largest commercial and recreational fisheries. Their extensive migratory patterns expose them to multiple national and international fisheries and fishery management regimes. Several prized species have become the focus of global conservation efforts and there is a growing worldwide interest in establishing optimal strategies for sustainable tuna fisheries. Although this task has proven to be very challenging, it has taken on a new sense of urgency in the face of the potential effects of global climate change. A better understanding of the interactions between environmental conditions and tuna physiology and how they affect tuna behavior will offer population and stock assessment modelers and fisheries biologists a more mechanistic understanding of tuna distribution patterns and may help predict changes in both geographic and depth-related movement patterns. Indeed, physiological data comprise a growing component of multi-trait analysis approaches to species conservation. Our review aims to summarize what is known about differences among tuna species in distribution patterns, tolerances to environmental conditions, and physiological characteristics that correlate with the capacity to inhabit cooler (deeper, higher latitude) and even hypoxic waters. To achieve this goal, we discuss how these physiological traits are associated with habitat partitioning within the three-dimensional oceanic environment and with niche expansion into cooler and hypoxic waters. We also point out areas where additional research is needed to predict more accurately how future changes in oceanographic conditions will affect the distributions and movement patterns of tunas and their availability to fisheries.     

Scientometric analysis of freshwater fisheries in Brazil: repeating past errors?

Freshwater fisheries are mainly small-scale activities and occur mostly in developing countries. These fisheries are recognized for its chronic lack of data and incipient knowledge when compared to large-scale fisheries, despite its socioeconomic and food security relevance. Brazil is a good model of small-scale freshwater fisheries country because it shares similar characteristics and shortcomings of many other countries in South America, Africa and Asia, where these activities prevail. This work aims to carry out a broad and comprehensive analysis of the approaches and limitations of Brazilian freshwater fisheries studies through a scientometric analysis. We conducted an exhaustive survey of scientific platforms such as the Web of Knowledge Thomson Reuters (ISI), Scientific Electronic Library Online (SciELO), Google Scholar and CNPq Lattes Curriculum Vitae Database. We found that the platforms ISI and SciELO were limited for this area of knowledge as they recovered only 47 % of the 186 studies reviewed. Brazilian freshwater fisheries studies were published in 72 journals and were conducted by 234 researchers, with very few specialists. On average the data processing into scientific information took 5 years, and half of the studies were conducted in short time scale (less than 2 years long) mostly by research institutions and universities. The number studies declined since the year 2008, after the creation of the Ministry of Fisheries and Aquiculture, which indicate that the fallacy of disregarding scientific knowledge may be permeating decision making agencies as already happen in the past in Brazil. The combination of these factors may cause slow and inefficient decision-making and management based on the best available science. Our results also highlighted the importance of multidisciplinarity in the training of human resources to work in the fishing sector.     

Partial migration in fishes: causes and consequences

Partial migration, where only some individuals from a population migrate, has been widely reported in a diverse range of animals. In this paper, what is known about the causes and consequences of partial migration in fishes is reviewed. Firstly, the ultimate and proximate drivers of partial migration are reflected upon: what ecological factors can shape the evolution of migratory dimorphism? How is partial migration maintained over evolutionary timescales? What proximate mechanisms determine whether an individual is migratory or remains resident? Following this, the consequences of partial migration are considered, in an ecological and evolutionary context, and also in an applied sense. Here it is argued that understanding the concept of partial migration is crucial for fisheries and ecosystem managers, and can provide information for conservation strategies. The review concludes with a reflection on the future opportunities in this field, and the avenues of research that are likely to be fruitful to shed light on the enduring puzzle of partial migration in fishes.     

Managing the fisheries by social engineering: a re-evaluation of the methods of stock assessment

This paper criticises the management of the world's fisheries that are based upon the use of 'positive' predictions derived from fisheries models, an instrumentalist approach which is illustrated by the practical application of Graham-Schaefer models constructed according to the verificationist's view of science. Instrumentalism is attractive for stock assessment because it appears to meet the need to overcome barriers within fisheries science to the deduction of specific predictions from universal laws. Through the construction of empirical models, existential predictions are produced which ape the specific predictions of the physical sciences and are of no more value in the management of the world's fisheries than the magic spells of witch doctors. To be contrasted with instrumentalism's prophetic use of 'positive' predictions, Karl Popper advocated a realist approach in which theoretical models help us gain factual information about the real-world in the form of what cannot be achieved : 'negative' explanatory predictions produced by models constructed according to the falsificationist's view of science and illustrated by the practical application of theoretical Gordon-Schaefer fisheries models.
The absence within fisheries stock assessment of a suitable alternative to instrumentalism comprises a widespread methodological lacuna. It is proposed that Popper's technological social science, designed to solve problems of social tradition of which overfishing is an example, would fill this lacuna. This technology would employ the services of a social engineer, a modern fisheries manager , who would use the pre-scientific method of trial and error and the negative guidance of bold pattern predictions to re-evaluate the institutions of fisheries management.     

Artisanal Fisheries Research: A Need for Globalization?

Given limited funds for research and widespread degradation of ecosystems, environmental scientists should geographically target their studies where they will be most effective. However, in academic areas such as conservation and natural resource management there is often a mismatch between the geographic foci of research effort/funding and research needs. The former frequently being focused in the developed world while the latter is greater in the biodiverse countries of the Global South. Here, we adopt a bibliometric approach to test this hypothesis using research on artisanal fisheries. Such fisheries occur throughout the world, but are especially prominent in developing countries where they are important for supporting local livelihoods, food security and poverty alleviation. Moreover, most artisanal fisheries in the Global South are unregulated and unmonitored and are in urgent need of science-based management to ensure future sustainability. Our results indicate that, as predicted, global research networks and centres of knowledge production are predominantly located in developed countries, indicating a global mismatch between research needs and capacity.     

Causes and consequences of winter mortality in fishes

Winter mortality has been documented in a large number of freshwater fish populations, and a smaller, but increasing, number of marine and estuarine fishes. The impacted populations include a number of important North American and European resource species, yet the sources of winter mortality remain unidentified in most populations where it has been documented. Among the potential sources, thermal stress and starvation have received the most research attention. Other sources including predation and pathogens have significant impacts but have received insufficient attention to date. Designs of more recent laboratory experiments have reflected recognition of the potential for interactions among these co-occurring stressors. Geographic patterns in winter mortality are, in some cases, linked to latitudinal clines in winter severity and variability. However, for many freshwater species in particular, the effects of local community structure (predators and prey) may overwhelm latitudinal patterns. Marine (and estuarine) systems differ from freshwater systems in several aspects important to overwintering fishes, the most important being the lack of isolating barriers in the ocean. While open population boundaries allow fish to adopt migration strategies minimizing exposure to thermal stresses, they may retard rates of evolution to local environments. Geographic patterns in the occurrence and causes of winter mortality are ultimately determined by the interaction of regional and local factors. Winter mortality impacts population dynamics through episodic depressions in stock size and regulation of annual cohort strength. While the former tends to act in a density-independent manner, the latter can be density dependent, as most sources of mortality tend to select against the smallest members of the cohort and population. Most stock assessment and management regimes have yet to explicitly incorporate the variability in winter mortality. Potential management responses include postponement of cohort evaluation (to after first winter of life), harvest restrictions following mortality events and habitat enhancement. Future research should place more emphasis on the ecological aspects of winter mortality including the influences of food-web structure on starvation and predation. Beyond illuminating an understudied life-history phase, studies of overwintering ecology are integral to contemporary issues in fisheries ecology including ecosystem management, habitat evaluation, and impacts of climate change.     

Estimating Fish Exploitation and Aquatic Habitat Loss across Diffuse Inland Recreational Fisheries

The current state of many freshwater fish stocks worldwide is largely unknown but suspected to be vulnerable to exploitation from recreational fisheries and habitat degradation. Both these factors, combined with complex ecological dynamics and the diffuse nature of inland fisheries could lead to an invisible collapse: the drastic decline in fish stocks without great public or management awareness. In this study we provide a method to address the pervasive knowledge gaps in regional rates of exploitation and habitat degradation, and demonstrate its use in one of North America’s largest and most diffuse recreational freshwater fisheries (Ontario, Canada). We estimated that 1) fish stocks were highly exploited and in apparent danger of collapse in management zones close to large population centres, and 2) fish habitat was under a low but constant threat of degradation at rates comparable to deforestation in Ontario and throughout Canada. These findings confirm some commonly held, but difficult to quantify, beliefs in inland fisheries management but also provide some further insights including 1) large anthropogenic projects greater than one hectare could contribute much more to fish habitat loss on an area basis than the cumulative effect of smaller projects within one year, 2) hooking mortality from catch-and-release fisheries is likely a greater source of mortality than the harvest itself, and 3) in most northern management zones over 50% of the fisheries resources are not yet accessible to anglers. While this model primarily provides a framework to prioritize management decisions and further targeted stock assessments, we note that our regional estimates of fisheries productivity and exploitation were similar to broadscale monitoring efforts by the Province of Ontario. We discuss the policy implications from our results and extending the model to other jurisdictions and countries.     

Automated species identification: why not?

Where possible, automation has been a common response of humankind to many activities that have to be repeated numerous times. The routine identification of specimens of previously described species has many of the characteristics of other activities that have been automated, and poses a major constraint on studies in many areas of both pure and applied biology. In this paper, we consider some of the reasons why automated species identification has not become widely employed, and whether it is a realistic option, addressing the notions that it is too difficult, too threatening, too different or too costly. Although recognizing that there are some very real technical obstacles yet to be overcome, we argue that progress in the development of automated species identification is extremely encouraging that such an approach has the potential to make a valuable contribution to reducing the burden of routine identifications. Vision and enterprise are perhaps more limiting at present than practical constraints on what might possibly be achieved.     

Searching for responsible and sustainable recreational fisheries in the Anthropocene

Recreational fisheries that use rod and reel (i.e., angling) operate around the globe in diverse freshwater and marine habitats, targeting many different gamefish species and engaging at least 220 million participants. The motivations for fishing vary extensively; whether anglers engage in catch-and-release or are harvest-oriented, there is strong potential for recreational fisheries to be conducted in a manner that is both responsible and sustainable. There are many examples of recreational fisheries that are well-managed where anglers, the angling industry and managers engage in responsible behaviours that both contribute to long-term sustainability of fish populations and the sector. Yet, recreational fisheries do not operate in a vacuum; fish populations face threats and stressors including harvest from other sectors as well as environmental change, a defining characteristic of the Anthropocene. We argue that the future of recreational fisheries and indeed many wild fish populations and aquatic ecosystems depends on having responsible and sustainable (R&S) recreational fisheries whilst, where possible, addressing, or at least lobbying for increased awareness about the threats to recreational fisheries emanating from outside the sector (e.g., climate change). Here, we first consider how the concepts of R&S intersect in the recreational fishing sector in an increasingly complex socio-cultural context. Next, we explore the role of the angler, angling industry and decision-makers in achieving R&S fisheries. We extend this idea further by considering the consequences of a future without recreational fisheries (either because of failures related to R&S) and explore a pertinent case study situated in Uttarakahand, India. Unlike other fisheries sectors where the number of participants is relatively small, recreational angling participants are numerous and widespread, such that if their actions are responsible, they have the potential to be a key voice for conservation and serve as a major force for good in the Anthropocene. What remains to be seen is whether this will be achieved, or if failure will occur to the point that recreational fisheries face increasing pressure to cease, as a result of external environmental threats, the environmental effects of recreational fishing and emerging ethical concerns about the welfare of angled fish.     

Conservation of Aquatic Resources through the Use of Freshwater Protected Areas: Opportunities and Challenges

Freshwater environments are currently experiencing an alarming decline in biodiversity. As a result, scientists and managers must look for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater environments from numerous threats is the use of freshwater protected areas (FPAs). FPAs are portions of the freshwater environment partitioned to minimize disturbances and allow natural processes to govern populations and ecosystems. While similar conservation practices are well established in the terrestrial and marine environments, the use of FPAs for conservation of freshwater environments has been relatively slow. Despite this, numerous examples exist in which FPAs have been incorporated into successful management approaches for freshwater environments. In this paper, we outline some of the past success stories where FPAs have been used to protect freshwater environments, discuss some of the reasons that this technique has not proliferated to the same degree as marine protected areas, and present some of the challenges that managers and scientists must overcome if they wish to implement FPAs. We recommend that the term Freshwater Protected Area be adopted to such conservation efforts, thereby standardizing terminology and facilitating literature searches and dissemination of research findings. Furthermore, we encourage freshwater scientists, conservationists and managers to develop and implement FPAs in innovative and creative situations thereby permitting the growth of the research base for this valuable conservation technique.     

Evaluating Potential Effects of Exotic Freshwater Fish From Incomplete Species Presence–absence Data

Many freshwater ecosystems and biotas around the world are threatened with extinction. Freshwater fishes, for example, are the most endangered vertebrates after amphibians. Exotic fish are widely recognized as a major disturbance agent for native fish. Evaluating the ecological effects of invaders presents many challenges and the problem is greatly augmented in parts of the world where the native fauna is poorly known and where exotic species are commonplace. We use the fish community of Patagonia, a small and distinct native biota dominated by exotic salmonids, as a case study to ask: what can we learn about the effects of exotic fish species from fragmentary or partial data and how do such data point the way to what needs to be learned? We review the available data and literature on the distribution and status of native and introduced fish. We compile a novel regional presence/absence species database, build fish distribution maps, describe distribution patterns of native and exotic species, and identify critical information voids. A comparative review of literature from Patagonia and Australasia, where a similar native and exotic fish fauna is found, helps us to identify research priorities and promising management strategies for the conservation of native fish fauna. We conclude that the main challenge for fish conservation in Patagonia is to identify management strategies that could preserve native species while maintaining the quality of salmonid fisheries.     

Pulmonate phylogeny based on 28S rRNA gene sequences: a framework for discussing habitat transitions and character transformation

Pulmonate snails occupy a wide range of marine, estuarine, freshwater and terrestrial environments. Non-terrestrial forms are supposed to be basal in pulmonate evolution but the group's phylogeny is not well resolved either morphologically or on the basis of available DNA sequence data. The lack of a robust phylogeny makes it difficult to understand character polarization and habitat transformation in pulmonates. We have investigated pulmonate relationships using 27 new sequences of 28S rRNA from pulmonates and outgroups, augmented with data from GenBank. The complete alignments comprised about 3.8kb. Maximum parsimony, maximum likelihood and Bayesian analyses of alignments generated under different assumptions are reported. Complete alignments appear to have a degree of substitution saturation so where there is conflict between hypothesised relationships more weight is given to analyses where regions of random similarity are excluded and which are not affected by this complication. Monophyly of the five main pulmonate groups was robustly supported in almost all analyses. The marine group Amphiboloidea and the freshwater Glacidorbidae are the most basal. The remaining pulmonates (Siphonariidae, Hygrophila and Eupulmonata) form a moderately-supported monophyletic group in all analyses bar one probably affected by saturation of substitutions. Siphonariidae, a predominantly marine and intertidal family, and Eupulmonata (mainly terrestrial with marine, estuarine and freshwater species) form a strongly supported clade that is the sister group to Hygrophila (freshwater). Multiple colonizations of freshwater and terrestrial habitats by pulmonate snails are suggested. No analyses strongly support the possibility of habitat reversions. The colonizations of freshwater by Hygrophila and of land by Stylommatophora were apparently phylogenetically independent although it cannot yet be excluded that there were transient terrestrial phases in the history of the former group or freshwater phases in the latter.     

Regulation of local mRNA translation

Regulated local mRNA translation is one mechanism cells employ to concentrate proteins in particular locations. However, cells use many different strategies to accomplish this task; for example, some mRNAs are destroyed in regions where they are not wanted, other mRNAs are repressed in areas where their translation would be deleterious, and yet other mRNAs are transported, in a quiescent state, to the sites where their translation is activated. The importance of local translation cannot be overstated, for, depending on the species or cell type, it is required for cell division, establishment of mating type, development and memory formation.     

Pitfalls of hypothesis tests and model selection on bootstrap samples: Causes and consequences in biometrical applications

The bootstrap method has become a widely used tool applied in diverse areas where results based on asymptotic theory are scarce. It can be applied, for example, for assessing the variance of a statistic, a quantile of interest or for significance testing by resampling from the null hypothesis. Recently, some approaches have been proposed in the biometrical field where hypothesis testing or model selection is performed on a bootstrap sample as if it were the original sample. P‐values computed from bootstrap samples have been used, for example, in the statistics and bioinformatics literature for ranking genes with respect to their differential expression, for estimating the variability of p‐values and for model stability investigations. Procedures which make use of bootstrapped information criteria are often applied in model stability investigations and model averaging approaches as well as when estimating the error of model selection procedures which involve tuning parameters. From the literature, however, there is evidence that p‐values and model selection criteria evaluated on bootstrap data sets do not represent what would be obtained on the original data or new data drawn from the overall population. We explain the reasons for this and, through the use of a real data set and simulations, we assess the practical impact on procedures relevant to biometrical applications in cases where it has not yet been studied. Moreover, we investigate the behavior of subsampling (i.e., drawing from a data set without replacement) as a potential alternative solution to the bootstrap for these procedures.     

Understanding and managing enhancements: why fisheries scientists should care

Fisheries enhancements are a set of management approaches involving the use of aquaculture technologies to enhance or restore fisheries in natural ecosystems. Enhancements are widely used in inland and coastal fisheries, but have received limited attention from fisheries scientists. This paper sets out 10 reasons why fisheries scientists should care about understanding and managing enhancements. (1) Enhancements happen, driven mostly by resource users and managers rather than scientists. (2) Enhancements create complex fisheries systems that encompass and integrate everything fisheries stakeholders can practically manage. (3) Enhancements emerge in fisheries where the scope for technical and governance control is high, and they synergistically reinforce both. (4) Successful enhancements expand management options and achievable outcomes. (5) Many enhancements fail or do ecological harm but persist regardless. (6) Effective science engagement is crucial to developing beneficial enhancements and preventing harmful ones. (7) Good scientific guidance is available to aid development or reform of enhancements but is not widely applied. (8) Enhancement research advances, integrates and unifies the fisheries sciences. (9) Enhancements provide unique opportunities for learning about natural fish populations and fisheries. (10) Needs, opportunities and incentives for enhancements are bound to increase.     

Positive relationships between genetic diversity and abundance in fishes

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and ‘abundance’ compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.