Whakapapa – A Foundation for Genetic Research?

Whakapapa is the foundation of traditional Māori social structure and it perpetuates a value base that locates people through their relationships to the physical and spiritual worlds. As part of a new envirogenomics research programme, researchers at the Institute of Environmental Science and Research (ESR) are developing a study with an iwi (tribe) to identify combinations of genetic and environmental factors that may contribute to current health status. A major objective of this study is to utilise whakapapa (genealogical information) to explore patterns of genetic variation unique to the iwi and to correlate these with potential disease or ill health. Genetic testing and screening raises numerous ethical issues, particularly when indigenous peoples are the subjects. This paper will outline ESR’s strategy for addressing indigenous concerns about genetic testing and how whakapapa forms an integral part of the envirogenomics research programme.     

Cephalopod and Groundfish Landings: Evidence for Ecological Change in Global Fisheries?

Cephalopod fisheries are among the few still with some local potential for expansion; in fact, as groundfish landings have declined globally, cephalopod landings have increased. We propose the hypothesis that, although increased cephalopod landings may partly reflect increased market demand, overfishing groundfish stocks has positively affected cephalopod populations. Data from 15 key FAO areas reveal that, with the exception of the north- east Atlantic, cephalopod landings have increased significantly over the last 25 years while groundfish have risen more slowly, remained stable, or declined. In terms of volume, cephalopods have not replaced groundfish. This is hypothesized as owing to the shorter life cycle of cephalopods, and rapid turnover and lower standing stocks than for longer-lived finfish species. Under high fishing pressure, groundfish are probably poor competitors, having less opportunity for spawning and replacement. In West Africa, the Gulf of Thailand and Adriatic there is strong circumstantial evidence that fishing pressure has changed ecological conditions and cephalopod stocks have increased as predatory fish have declined. We recommend that this hypothesis be tested thoroughly in other areas where suitable data exist. Most coastal and shelf cephalopod fisheries are likely to be fully exploited or overexploited, and current annual fluctuations in cephalopod landings are probably largely environmentally-driven.     

Biodiversity Offsets: A Cost-Effective Interim Solution to Seabird Bycatch in Fisheries?

The concept of biodiversity offsets is well established as an approach to environmental management. The concept has been suggested for environmental management in fisheries, particularly in relation to the substantial numbers of non-target species--seabirds in particular--caught and killed as incidental bycatch during fishing activities. Substantial areas of fisheries are being closed to protect these species at great cost to the fishing industry. However, other actions may be taken to offset the impact of fishing on these populations at lower cost to the fishing industry. This idea, however, has attracted severe criticism largely as it does not address the underlying externality problems created by the fishing sector, namely seabird fishing mortality. In this paper, we re-examine the potential role of compensatory mitigation as a fisheries management tool, although from the perspective of being an interim management measure while more long-lasting solutions to the problem are found. We re-model an example previously examined by both proponents and opponents of the approach, namely the cost effectiveness of rodent control relative to fishery area closures for the conservation of a seabird population adversely affected by an Australian tuna fishery. We find that, in the example being examined, invasive rodent eradication is at least 10 times more cost effective than area closures. We conclude that, while this does not solve the actual bycatch problem, it may provide breathing space for both the seabird species and the industry to find longer term means of reducing bycatch.     

Maine's Baitworm Fisheries: Resources at Risk?

Two species of polychaetous annelids are dug for sale as baitfrom intertidal mudflats of Maine. This effort generatesnearly$3.5 million in annual revenue and comprises over 90% of thebaitworm fisheries in the U.S. The two species are (1) sandwormsor clamworms, Nereis virens (family Nereididae) and (2) bloodwormsor beakworms, Glycera dibranchiata (family Glyceridae). Numbersof baitworm diggers licensed annually in Maine have increasedfrom 449 in 1948 to a maximum of 1,455 in 1974 and decreasedsince then to 801 in 1991. Sandworm landings increased fromthe late 1940s until the early 1960s when they leveled off.They fluctuated between 300,000 and 400,000 lbs landed annuallyfor the next 20 years. Between 1982 and 1991, the sandworm landingsranged between 179,000 (1990) and 380,000 (1982) lbs landedper year. Bloodworm landings were at a maximum between 1960and 1976, ranging between 140,000 and 215,000 lbs landed annually.After a sharp decline in the bloodworm fishery in the late 1970s,annual landings ranged between 102,000 (1988) and 168,000 (1982)lbs. Reasons for the fluctuations and recent decreases in landingsremain unexplained. Some data suggest that market demand limitsthe baitworm landings for both species, while others imply thatoverharvesting, at least for bloodworms, may be a problem forthese resources.     

Where Next for Microbiome Research?

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of “van Leeuwenhoek”–like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what’s next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.

This Perspective is part of the “Where next?” Series.

Soon, we will enter an era when “the number of population genomes deposited in public databases will dwarf those from isolates and single cells” (Gene Tyson). Clearly, as all authors noted in the following, our focus will move from describing the composition of microbial communities to elucidating the principles that govern their assembly, dynamics, and functions. How will such principles be discovered? Elhanan Borenstein proposes that a systems biology–based approach, particularly the development of mathematical and computational models of the interactions between the specific community components, will be critical for understanding the function and dynamics of microbiomes. Evolutionary biologists Howard Ochman and Andrew Moeller want to decipher how microbial assemblies evolve but challenge us to also consider the role of microbial communities in organismal evolution, and they make the exciting prediction that microbes will be implicated in the evolution of eusociality and cooperation. Brett Finlay underscores the need for deciphering the mechanistic bases—particularly the chemical/metabolite signals—for interactions between members of microbial communities and their hosts. He emphasizes how this knowledge will enable creation of new tools to manipulate the microbiota, a key challenge for future investigation. Heidi Kong also encourages deciphering the mechanisms that underlie associations between particular skin surfaces and disorders and their respective microbiota. Jeffrey Gordon considers several intriguing opportunities as well as challenges that manipulation of the gut microbiota presents for improved human nutrition and health. Finally, Karen Nelson, Karim Dabbagh and Hamilton Smith suggest that using synthetic genomes to create novel microbes or even synthetic microbiomes offers a new way to engineer the microbiota. Overall, future microbiome research regarding the molecules and mechanisms mediating interactions between members of microbial communities and their hosts should lead to discovery of exciting new biology and transformative therapeutics.     

Taurine-reduction Powers Rapid Growth of Bilophila wadsworthia: A Liquid Minimal-salts Medium for Clinical Research?

Clinical isolates of Bilophila wadsworthia grew rapidly (1–3 days) in the liquid taurine-minimal-salts medium developed for B. wadsworthia RZATAU, whereas growth on Bacteroides Bile Esculin Agar takes up to 1 week. Though rapid growth of B. wadsworthia was achieved, and no other pure cultures grew, the medium was not selective for the organism in human faeces or in intra-abdominal specimens. We hope, however, that our understanding of the physiological and biochemical characteristics of the organism supplies a tool for further research.     

Is There a Global Market for Tuna? Policy Implications for Tropical Tuna Fisheries

Regional ex-vessel markets for cannery-grade skipjack tuna throughout the globe are spatially integrated by price, but such markets for yellowfin tuna are spatially independent. The Americas exert primary price leadership in ex-vessel skipjack markets, but Bangkok and American Samoa also exert price leadership, and Ivory Coast, Japan, and Spain are largely price followers. Regional ex-vessel markets for skipjack and yellowfin are not integrated by prices. While price effects of this nature are simply evidence of a pecuniary externality, and thereby do not necessarily affect the overall size of global net benefits, in practice such price effects affect distribution among players—who wins and who loses—and in this manner, the eventual formation of, and compliance with, different management policies.     

Fisheries bioeconomics: why is it so widely misunderstood?

Many fisheries management systems, even when based on apparently sound science, have failed to prevent severe overfishing. And even when successful in this sense, such systems have frequently resulted in a large degree of excess fishing capacity. The reason for these failures can often be found in a lack of consideration of the economic incentives affecting fishermen. Specifically, when forced to compete for a fixed total annual catch quota (TAC), fishermen are motivated to fish at high intensity, and to expand the fishing power of their vessels. Individual fishing quotas (IFQs) are being increasingly used as a method of altering economic incentives in a desirable way. IFQ systems, however, can also suffer severe shortcomings, unless substantial fees are extracted for the exclusive right to exploit a publicly owned resource. When combined with appropriate fees, or royalties, IFQs can indeed result in sustainable, profitable fisheries. There still remains the fundamental question of risk management, but this is also now beginning to be addressed. Thus there is now a strong hope for the future success of marine fisheries, at least within 200-mile coastal zones.     

2010: A new beginning for biodiversity?

Proclaimed “International Year of Biodiversity”, will 2010 hold all its promises? Reminder: initiated by the Convention on Biological Diversity ratified after the global summit in Rio de Janeiro, delegations from more than one hundred countries gathered in Johannesburg in 2002 and committed themselves to slowing the erosion of biodiversity by 2010. The European Union was more ambitious (or reckless?) and even spoke about halting this erosion (European Environment Agency, Progress towards the European 2010 biodiversity target, 2009) [1]! Well, that date has come and the overall appraisal that has been made formally in Nagoya in October this year was not so brilliant (see Leadley et al., 2010) [2]–but the same slogan has been launched for 2020! The aim here is not to repeat that appraisal, but, after considering the broad outlines, to evoke some of the issues and challenges that inevitably result from the great question of the protection and management of global biodiversity.     

Adiponectin: A biomarker for rheumatoid arthritis?

Recent achievements in the biology and the function of adipose tissue have regarded white adipose tissue (WAT) as an important endocrine and secretory organ. Releasing a series of multiple-function mediators, WAT is involved in a wide spectrum of diseases, including not only cardiovascular and metabolic complications, such as atherosclerosis and type 2 diabetes, but also inflammatory- and immune-related disorders, such as rheumatoid arthritis (RA) and osteoarthritis (OA). A large number of these mediators, called adipokines, such as tumor necrosis factor alpha (TNF-α), leptin, adiponectin, resistin, chemerin, interleukin-6 (IL-6), visfatin, and so on have been identified and studied widely. Important advances related to these proteins shed new insights into the pathophysiological mechanisms of many complicated diseases, although details of which remain unclear. Adiponectin, one of the most widely investigated adipokine, has been shown to possess both anti- and pro-inflammatory effects. RA is a chronic systemic inflammatory-related autoimmune disease. Accumulated evidence has demonstrated that cytokines and adipokines play an important role in the pathogenesis of RA. In this review, we have summarized the most recent advances in adiponectin research in the context of RA, focusing primarily on its effect on RA-related cells, its regulation on pro-inflammatory cytokines, as well as its validation as a biomarker for RA.