Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach

BACKGROUND

Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students.

RESULTS

We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools.

CONCLUSION

Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.

Educating for the marine environment: Challenges for schools and scientists

Environmental education has long been recognized as critical for achieving environmental awareness, values and attitudes, skills and behaviour consistent with sustainable development and for effective participation in environmental decision-making. Since the Declaration of the 1972 United Nations Conference on the Human Environment concerns about marine pollution and ecotoxicology, among other environmental challenges, should be included in environmental education. However, in the more than forty years since this significant environmental Declaration, marine education has struggled to find a place in the school curriculum of most countries, even though issues such as climate change, chemical contamination of marine environments, coastal eutrophication, and seafood safety continue to threaten human and other species' well-being. This viewpoint discusses how marine education is marginalized in school education, and how marine specialists need to embed school education in their action plans. Particular questions include: who should be educated, about what, where and with what goals in mind?

A Citizen Science Approach: A Detailed Ecological Assessment of Subtropical Reefs at Point Lookout, Australia

Subtropical reefs provide an important habitat for flora and fauna, and proper monitoring is required for conservation. Monitoring these exposed and submerged reefs is challenging and available resources are limited. Citizen science is increasing in momentum, as an applied research tool and in the variety of monitoring approaches adopted. This paper aims to demonstrate an ecological assessment and mapping approach that incorporates both top-down (volunteer marine scientists) and bottom-up (divers/community) engagement aspects of citizen science, applied at a subtropical reef at Point Lookout, Southeast Queensland, Australia. Marine scientists trained fifty citizen scientists in survey techniques that included mapping of habitat features, recording of substrate, fish and invertebrate composition, and quantifying impacts (e.g., occurrence of substrate damage, presence of litter). In 2014 these volunteers conducted four seasonal surveys along semi-permanent transects, at five sites, across three reefs. The project presented is a model on how citizen science can be conducted in a marine environment through collaboration of volunteer researchers, non-researchers and local marine authorities. Significant differences in coral and algal cover were observed among the three sites, while fluctuations in algal cover were also observed seasonally. Differences in fish assemblages were apparent among sites and seasons, with subtropical fish groups observed more commonly in colder seasons. The least physical damage occurred in the most exposed sites (Flat Rock) within the highly protected marine park zones. The broad range of data collected through this top-down/bottom-up approach to citizen science exemplifies the projects’ value and application for identifying ecosystem trends or patterns. The results of the project support natural resource and marine park management, providing a valuable contribution to existing scientific knowledge and the conservation of local reefs.

On the apparent failure of silt fences to protect freshwater ecosystems from sedimentation: A call for improvements in science, technology, training and compliance monitoring

Excessive sedimentation derived from anthropogenic activities is a main factor in habitat and biodiversity loss in freshwater ecosystems. To prevent offsite movement of soil particles, many environmental regulatory agencies mandate the use of perimeter silt fences. However, research regarding the efficiency of these devices in applied settings is lacking, and fences are often ineffective due to poor installation and maintenance. Here, we provide an overview of the current state of research regarding silt fences, address the current culture surrounding silt fence installation and maintenance, and provide several recommendations for improving the knowledge base related to silt fence effectiveness. It is clear that there is a need for integrated long-term (i.e., extending from prior to fence installation to well after fence removal) multi-disciplinary research with appropriate controls that evaluates the effectiveness of silt control fences. Through laboratory experiments, in silico modelling and field studies there are many factors that can be experimentally manipulated such as soil types (and sediment feed rate), precipitation regimes (and flow rate), season, slope, level of site disturbance, fence installation method, type of fence material, depth of toe, type and spacing of support structures, time since installation, level of inspection and maintenance, among others, that all require systematic evaluation. Doing so will inform the practice, as well as identify specific technical research needs, related to silt fence design and use. Moreover, what constitutes "proper" installation and maintenance is unclear, especially given regional- and site-level variation in precipitation, slope, and soil characteristics. Educating and empowering construction crews to be proactive in maintenance of silt fencing is needed given an apparent lack of compliance monitoring by regulatory agencies and the realities that the damage is almost instantaneous when silt fences fail. Our goal is not to dismiss silt fences as a potentially useful tool. Instead, we question the way they are currently being used and call for better science to determine what factors (in terms of fence design, installation and site-characteristics) influence effectiveness as well as better training for those that install, maintain and inspect such devices. We also encourage efforts to "look beyond the fence" to consider how silt fences can be combined with other sediment control strategies as part of an integrated sediment control program.

[The sea in the museum: a perspective on education at aquariums]

The musealization of the sea, today spearheaded by aquariums and oceanariums, encapsulated man's relationship with these environments and the techniques used to explore them and keep organisms alive in captivity. Recognizing the combined roles of research and entertainment at aquariums, some aspects of their constitution over time are analyzed, especially the education and communication dimensions they have focused on more in recent times. For this purpose, we investigate in detail a Brazilian institution, Ubatuba Aquarium, indicating how its musealization incorporates clear intentions to promote education and communication in subjects from the realms of zoology, ecology and conservation.

The GRS/GRC from the perspective of a graduate student and first time attendee

The networking and collaborative opportunities afforded to the attendees of the Ocean and Human Health Gordon Research Seminar (GRS) and the Gordon Research Conference (GRC) are vast and great. The GRS/GRC, in particular, has the capability of facilitating interlaboratory and interdisciplinary collaborations. The following article highlights the benefits associated with attending the GRS/GRC as a graduate student and first time attendee.

A perspective on the history and evolution of an Oceans and Human Health "metadiscipline" in the USA

We review recent history and evolution of Oceans and Human Health programs and related activities in the USA from a perspective within the Federal government. As a result of about a decade of support by the US Congress and through a few Federal agencies, notably the National Science Foundation, National Institute of Environmental Health Sciences, and National Ocean and Atmospheric Administration, robust Oceans and Human Health (OHH) research and application activities are now relatively widespread, although still small, in a number of agencies and academic institutions. OHH themes and issues have been incorporated into comprehensive federal ocean research plans and are reflected in the new National Ocean Policy enunciated by Executive Order 13547. In just a decade, OHH has matured into a recognized "metadiscipline," with development of a small, but robust and diverse community of science and practice, incorporation into academic educational programs, regular participation in ocean and coastal science and public health societies, and active engagement with public health decision makers. In addition to substantial increases in scientific information, the OHH community has demonstrated ability to respond rapidly and effectively to emergency situations such as those associated with extreme weather events (e.g., hurricanes, floods) and human-caused disasters (e.g., the Deep Water Horizon oil spill). Among many other things, next steps include development and implementation of agency health strategies and provision of specific services, such as ecological forecasts to provide routine early warnings for ocean health threats and opportunities for prevention and mitigation of these risks.

What distinguishes the Gordon Research Conference on Oceans and Human Health? A retrospective 2008-2012

This piece is being submitted as a short commentary for the special edition on Oceans and Human Health (OHH). It is written from the perspective of a student who has attended all three biennial Gordon Research Conferences and Seminars on OHH beginning in 2008.

Illustrations and the genesis of Barrett and Yonge's "Collins pocket guide to the sea shore" (1958)

Twenty nine items of correspondence from the mid-1950s discovered recently in the archives of the University Marine Biological Station Millport, and others made available by one of the illustrators and a referee, shed unique light on the publishing history of "Collins pocket guide to the sea shore". This handbook, generally regarded as a classic of its genre, marked a huge step forwards in 1958; providing generations of students with an authoritative, concise, affordable, well illustrated text with which to identify common organisms found between the tidemarks from around the coasts of the British Isles. The crucial role played by a select band of illustrators in making this publication the success it eventually became, is highlighted herein. The difficulties of accomplishing this production within commercial strictures, and generally as a sideline to the main employment of the participants, are revealed. Such stresses were not helped by changing demands on the illustrators made by the authors and by the publishers.

Graphical methods and Cold War scientific practice: the Stommel Diagram's intriguing journey from the physical to the biological environmental sciences

In the last quarter of the twentieth century, an innovative three-dimensional graphical technique was introduced into biological oceanography and ecology, where it spread rapidly. Used to improve scientists' understanding of the importance of scale within oceanic ecosystems, this influential diagram addressed biological scales from phytoplankton to fish, physical scales from diurnal tides to ocean currents, and temporal scales from hours to ice ages. Yet the Stommel Diagram (named for physical oceanographer Henry Stommel, who created it in 1963) had not been devised to aid ecological investigations. Rather, Stommel intended it to help plan large-scale research programs in physical oceanography, particularly as Cold War research funding enabled a dramatic expansion of physical oceanography in the 1960s. Marine ecologists utilized the Stommel Diagram to enhance research on biological production in ocean environments, a key concern by the 1970s amid growing alarm about overfishing and ocean pollution. Before the end of the twentieth century, the diagram had become a significant tool within the discipline of ecology. Tracing the path that Stommel's graphical techniques traveled from the physical to the biological environmental sciences reveals a great deal about practices in these distinct research communities and their relative professional and institutional standings in the Cold War era. Crucial to appreciating the course of that path is an understanding of the divergent intellectual and social contexts of the physical versus the biological environmental sciences.

Marine birds as indicators of Arctic marine ecosystem health: linking the Northern Ecosystem Initiative to long-term studies

Marine birds are sensitive indicators of the condition of marine ecosystems in the Arctic, partly because they feed at the top of the arctic food chain. The Northern Ecosystem Initiative (NEI) recently supported four separate studies that investigated aspects of Arctic marine bird science which simultaneously addressed goals of the NEI to better understand northern ecosystems and their response to environmental stressors. The projects used both scientific and traditional knowledge to examine the relationship between sea-ice, contaminants, and the ecology of marine birds, and to transfer environmental knowledge to students. Results from these investigations confirm that changes are occurring in Arctic environments, and that these are captured through marine bird research. Collectively these studies provided new data that supported NEI objectives of monitoring the health of the Arctic ecosystem, and contributed to Canada's international obligations for Arctic science.

Marine biotechnology in education: a competitive approach

This paper describes the development of a practical, which is taught to third year biotechnology students. We wanted to motivate the students by making them responsible for a research project. Competition was added as a stimulus for interaction between the students. A virtual company called CaroTech employed the students for 2 weeks. They worked in groups of two persons and each group was responsible for a 0.8 l flat panel photobioreactor. They had to produce as much beta-carotene as possible using the marine alga strain Dunaliella salina in this photobioreactor. On the first day, students developed a strategy to obtain optimal algal growth rate. They putted this plan into practice the second day and while cultivating the organism, they developed a second strategy how and when to stress the alga to initiate beta-carotene production. At the end of the ninth day, the total amount of beta-carotene was measured. To stimulate competition, the group that produced the most beta-carotene obtained half a point bonus on the final practical mark. On the tenth day, each group presented their results and an evaluation of their chosen strategies to the CaroTech board. Most groups were successful in growing algae. In the second phase some groups failed to stress the alga. The best group produced more than two times beta-carotene than the runner-up. The students were motivated by being responsible for their own results and the competitive approach. All students liked the practical and indicated that they learned a lot by following this practical.

Entobdella soleae--pointers to the future

The biology of the monogenean skin parasite Entobdella soleae and its relationship with its host, the common sole (Solea solea), are probably better known than those of any other monogeneans. The author describes his early involvement with this parasite and the special features of parasite and host that make this relationship so suitable for parasitological studies. Aspects of the biology of E. soleae that have been investigated are briefly mentioned, but most of the paper is concerned with areas of the parasite's biology that remain a challenge to determine. Unresolved areas are as follows: (1) the identity of the factor (or factors) in host skin mucus that stimulates hatching of the parasite's eggs; (2) whether or not the larvae of the parasite are attracted to their host; (3) the nature of factors controlling the contrasting behaviour of adult parasites on the upper and lower surfaces of the host; (4) how nutrients are supplied to the remote regions of the haptor; (5) whether the host has any control via its immune system over parasite invasion success and survival; (6) how the parasite copes with the migratory habits of some sole populations, assuming that such populations are infested with the parasite. The intimacy of this parasite/host relationship is its most remarkable feature, the reflection of which, not surprisingly, is the greatly restricted host range of the parasite. E. soleae has been reported from only three host species, all highly specialised bottom-dwelling members of Solea. It is all the more surprising that relatives of E. soleae, such as Neobenedenia melleni, retain the ability to parasitise an enormous range of hosts. How this versatility is achieved remains to be seen.

Aquarium visitors' perceptions and attitudes toward the importance of marine biodiversity

To study people's perceptions and attitudes toward the importance of marine biodiversity, 102 visitors to San Francisco's UnderWater World aquarium were interviewed about their perceptions, attitudes, and knowledge about marine life and the environment needed for survival. They were asked about any changes in perceptions and attitudes after their visit. The data indicate that most visitors had very little education in marine biology, that 84% had previously visited other aquariums, that 98% had maintained or increased their positive attitudes toward marine life, and that only 20% financially or emotionally supported marine animal protection or preservation societies. These data, especially from people who had previously visited aquariums, indicated a need for school and college classes and texts to include more substantial and interest-stimulating information about the encompassing importance of the oceans for the survival of all terrestrial and oceanic species.