Using,risking, and consent: Why risking harm to bystanders is morally different from risking harm to research subjects

Subjects in studies on humans are used as a means of conducting the research and achieving whatever good would justify putting them at risk. Accordingly, consent must normally be obtained before subjects are exposed to any substantial risks to their welfare. Bystanders are also often put at risk, but they are not used as a means. Accordingly—or so I argue—consent is more often unnecessary before bystanders are exposed to similar substantial risks to their welfare.     

Landscape of ecological research in Australia: A bibliometric analysis of trends in research output and hotspots of research from 1991 to 2010

The spatial distribution and density of scientists can have important implications for key aspects of scientific processes, such as innovation, networking, rates of knowledge exchange and success in large competitive grants. In this paper, we examine the research output of different research organizations and universities in Australia, with the aim of identifying hotspots of ecological research and how these hotspots have changed over the last 20 years. We used publications from 10 reputable peer‐reviewed international journals as a measure of research output. We identified a number of ecology hotspot clusters. Some clusters have developed significantly over the last 20 years, while others have declined in output over time. The University of Sydney, University of Queensland, James Cook University and Melbourne University had the largest output levels among universities. Results also showed large increases in output over the last 5‐year period (2006–2010), possibly because of the impending introduction of the Excellence in Research for Australia.     

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host–microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage‐specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent‐gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host–microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis‐driven research.     

Leptin, from fat to inflammation: old questions and new insights

Leptin is 16 kDa adipokine that links nutritional status with neuroendocrine and immune functions. Initially thought to be a satiety factor that regulates body weight by inhibiting food intake and stimulating energy expenditure, leptin is a pleiotropic hormone whose multiple effects include regulation of endocrine function, reproduction, and immunity. Leptin can be considered as a pro-inflammatory cytokine that belongs to the family of long-chain helical cytokines and has structural similarity with interleukin-6, prolactin, growth hormone, IL-12, IL-15, granulocyte colony-stimulating factor and oncostatin M. Because of its dual nature as a hormone and cytokine, leptin links the neuroendocrine and the immune system. The role of leptin in the modulation of immune response and inflammation has recently become increasingly evident. The increase in leptin production that occurs during infection and inflammation strongly suggests that leptin is a part of the cytokine network which governs the inflammatory-immune response and the host defense mechanisms. Leptin plays an important role in inflammatory processes involving T cells and has been reported to modulate T-helper cells activity in the cellular immune response. Several studies have implicated leptin in the pathogenesis of autoimmune inflammatory conditions, such as experimental autoimmune encephalomyelitis, type 1 diabetes, rheumatoid arthritis, and intestinal inflammation. Very recently, a key role for leptin in osteoarthritis has been demonstrated: leptin indeed exhibits, in concert with other pro-inflammatory cytokines, a detrimental effect on articular cartilage by promoting nitric oxide synthesis in chondrocytes. Here, we review the recent advances regarding leptin biology with a special focus on those actions relevant to the role of leptin in the pathophysiology of inflammatory processes and immune responses.     

New insights from the last decade of research in psychiatric genetics: discoveries,challenges and clinical implications

Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.     

New insights from MALDI-ToF MS, NMR, and GC-MS: mass spectrometry techniques applied to palynology

Summary. The present study for the first time describes the application of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) to palynology. With an accessible mass range of up to about 350,000 Da at subpicomolar range, this technique is ideal for the characterisation of bio-macromolecules, such as sporopollenin, found in fossil and extant pollen and spore walls, which often can only be isolated in very small quantities. At this stage, the limited solubility of sporopollenin allows for the identification of sections of this biopolymer, but with the optimisation of MALDI-ToF matrices, further structure elucidation will become possible. Furthermore, gas chromatography–mass spectrometry (GC-MS) and ¹H nuclear magnetic resonance (¹H NMR) spectroscopy data obtained from a number of experiments revealed that some previously reported data were misinterpreted. These results add support to the hypothesis that common plasticizers were wrongly described as sporopollenin compounds. Correspondence and reprints: School of Earth, Ocean and Planetary Sciences, Cardiff University, Park Place, Cardiff CF10 3YE, United Kingdom. Permanent address: Albion College, Albion, Michigan, U.S.A.     

Global research trends and gaps in ecological compensation studies from 1990 to 2020: A scientometric review

Ecosystems are facing severe destruction and threats due to unreasonable human utilization. Repairing damage to nature and protect biodiversity through ecological compensation will be an inevitable measure for achieving sustainable development. To explore the current research hotspots and future research directions of ecological compensation, this paper tries to search the WoS Core Collection and collects 685 ecological compensation papers published between 1990 and 2020. R language and CiteSpace software were applied in this paper. It is found that: (1) The number of articles has gone through the initial explorations, fluctuating growth, and rapid development of the field from 1990 to 2020. Only 7.5% of authors have published more than two papers. (2) Regarding the production of papers, the top 3 countries are the US, China, and the UK. At present, the majority of countries focus on independent research, and international cooperation is gradually strengthening. (3) The current research hotpots mainly invlove biodiversity and sustainable development, ecological compensation for forests and water resources, China's Grain-to-Green Project, poverty reduction, livelihood issues, public participation willingness and equity issues, indicating that ecological compensation is a rapidly emerging interdisciplinary academic field. (4) The results reveal several research directions in the future: strengthening theoretical research, resolving issues pertaining to the complex relationships among stakeholders, encouraging a transformation from qualitative to quantitative research, increasing the focus of ecological compensation models on local conditions, and applying more scientific models and high-tech tools in effect evaluation.     

Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics

Introduction: The last 20 years have seen significant improvements in the analytical capabilities of biological mass spectrometry (MS). Studies using advanced MS have resulted in new insights into cell biology and the etiology of diseases as well as its use in clinical applications.

Areas covered: This review discusses recent developments in MS-based technologies and their cancer-related applications with a focus on proteomics. It also discusses the issues around translating the research findings to the clinic and provides an outline of where the field is moving.

Expert commentary: Proteomics has been problematic to adapt for the clinical setting. However, MS-based techniques continue to demonstrate potential in novel clinical uses beyond classical cancer proteomics.     

You are welcome here: A practical guide to diversity,equity, and inclusion for undergraduates embarking on an ecological research experience

As we build a more diverse, equitable, and inclusive culture in the ecological research community, we must work to support new ecologists by empowering them with the knowledge, tools, validation, and sense of belonging in ecology to succeed. Undergraduate research experiences (UREs) are critical for a student''s professional and interpersonal skill development and key for recruiting and retaining students from diverse groups to ecology. However, few resources exist that speak directly to an undergraduate researcher on the diversity, equity, and inclusion (DEI) dimensions of embarking on a first research experience. Here, we write primarily for undergraduate readers, though a broader audience of readers, especially URE mentors, will also find this useful. We explain many of the ways a URE benefits undergraduate researchers and describe how URE students from different positionalities can contribute to an inclusive research culture. We address three common sources of anxiety for URE students through a DEI lens: imposter syndrome, communicating with mentors, and safety in fieldwork. We discuss the benefits as well as the unique vulnerabilities and risks associated with fieldwork, including the potential for harassment and assault. Imposter syndrome and toxic field experiences are known to drive students, including students from underrepresented minority groups, out of STEM. Our goal is to encourage all students, including those from underrepresented groups, to apply for UREs, build awareness of their contributions to inclusion in ecology research, and provide strategies for overcoming known barriers.     

Bio-banking in microbiology: from sample collection to epidemiology, diagnosis and research

Millions of biological samples, including cells of human, animal or bacterial origin, viruses, serum/plasma or DNA/RNA, are stored every year throughout the world for diagnostics and research. The purpose of this review is to summarize the resources necessary to set up a bio-banking facility, the challenges and pitfalls of sample collection, and the most important techniques for separation and storage of samples. Biological samples can be stored for up to 30 years, but specific protocols are required to reduce the damage induced by preservation techniques. Software dedicated to biological banks facilitate sample registration and identification, the cataloguing of sample properties (type of sample/specimen, associated diseases and/or therapeutic protocols, environmental information, etc.), sample tracking, quality assurance and specimen availability. Bio-bank facilities must adopt good laboratory practices and a stringent quality control system and, when required, comply with ethical issues.     

Multiple successional pathways in human‐modified tropical landscapes: new insights from forest succession,forest fragmentation and landscape ecology research

Old‐growth tropical forests are being extensively deforested and fragmented worldwide. Yet forest recovery through succession has led to an expansion of secondary forests in human‐modified tropical landscapes (HMTLs). Secondary forests thus emerge as a potential repository for tropical biodiversity, and also as a source of essential ecosystem functions and services in HMTLs. Such critical roles are controversial, however, as they depend on successional, landscape and socio‐economic dynamics, which can vary widely within and across landscapes and regions. Understanding the main drivers of successional pathways of disturbed tropical forests is critically needed for improving management, conservation, and restoration strategies. Here, we combine emerging knowledge from tropical forest succession, forest fragmentation and landscape ecology research to identify the main driving forces shaping successional pathways at different spatial scales. We also explore causal connections between land‐use dynamics and the level of predictability of successional pathways, and examine potential implications of such connections to determine the importance of secondary forests for biodiversity conservation in HMTLs. We show that secondary succession (SS) in tropical landscapes is a multifactorial phenomenon affected by a myriad of forces operating at multiple spatio‐temporal scales. SS is relatively fast and more predictable in recently modified landscapes and where well‐preserved biodiversity‐rich native forests are still present in the landscape. Yet the increasing variation in landscape spatial configuration and matrix heterogeneity in landscapes with intermediate levels of disturbance increases the uncertainty of successional pathways. In landscapes that have suffered extensive and intensive human disturbances, however, succession can be slow or arrested, with impoverished assemblages and reduced potential to deliver ecosystem functions and services. We conclude that: (i) succession must be examined using more comprehensive explanatory models, providing information about the forces affecting not only the presence but also the persistence of species and ecological groups, particularly of those taxa expected to be extirpated from HMTLs; (ii) SS research should integrate new aspects from forest fragmentation and landscape ecology research to address accurately the potential of secondary forests to serve as biodiversity repositories; and (iii) secondary forest stands, as a dynamic component of HMTLs, must be incorporated as key elements of conservation planning; i.e. secondary forest stands must be actively managed (e.g. using assisted forest restoration) according to conservation goals at broad spatial scales.     

Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.     

Molecular cloning of alpha-amylases from cotton boll weevil,Anthonomus grandis and structural relations to plant inhibitors: an approach to insect resistance

Anthonomus grandis, the cotton boll weevil, causes severe cotton crop losses in North and South America. Here we demonstrate the presence of starch in the cotton pollen grains and young ovules that are the main A. grandis food source. We further demonstrate the presence of -amylase activity, an essential enzyme of carbohydrate metabolism for many crop pests, in A. grandis midgut. Two -amylase cDNAs from A. grandis larvae were isolated using RT-PCR followed by 5 and 3 RACE techniques. These encode proteins with predicted molecular masses of 50.8 and 52.7 kDa, respectively, which share 58% amino acid identity. Expression of both genes is induced upon feeding and concentrated in the midgut of adult insects. Several -amylase inhibitors from plants were assayed against A. grandis -amylases but, unexpectedly, only the BIII inhibitor from rye kernels proved highly effective, with inhibitors generally active against other insect amylases lacking effect. Structural modeling of Amylag1 and Amylag2 showed that different factors seem to be responsible for the lack of effect of 0.19 and -AI1 inhibitors on A. grandis -amylase activity. This work suggests that genetic engineering of cotton to express -amylase inhibitors may offer a novel route to A. grandis resistance.     

Forty years of carabid beetle research in Europe - from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

‘Carabidologists do it all’ (Niemelä 1996a) is a phrase with which most European carabidologists are familiar. Indeed, during the last half a century, professional and amateur entomologists have contributed enormously to our understanding of the basic biology of carabid beetles. The success of the field is in no small part due to regular European Carabidologists’ Meetings, which started in 1969 in Wijster, the Netherlands, with the 14th meeting again held in the Netherlands in 2009, celebrating the 40th anniversary of the first meeting and 50 years of long-term research in the Dwingelderveld. This paper offers a subjective summary of some of the major developments in carabidology since the 1960s. Taxonomy of the family Carabidae is now reasonably established, and the application of modern taxonomic tools has brought up several surprises like elsewhere in the animal kingdom. Progress has been made on the ultimate and proximate factors of seasonality and timing of reproduction, which only exceptionally show non-seasonality. Triggers can be linked to evolutionary events and plausibly explained by the “taxon cycle” theory. Fairly little is still known about certain feeding preferences, including granivory and ants, as well as unique life history strategies, such as ectoparasitism and predation on higher taxa. The study of carabids has been instrumental in developing metapopulation theory (even if it was termed differently). Dispersal is one of the areas intensively studied, and results show an intricate interaction between walking and flying as the major mechanisms. The ecological study of carabids is still hampered by some unresolved questions about sampling and data evaluation. It is recognised that knowledge is uneven, especially concerning larvae and species in tropical areas. By their abundance and wide distribution, carabid beetles can be useful in population studies, bioindication, conservation biology and landscape ecology. Indeed, 40 years of carabidological research have provided so much data and insights, that among insects - and arguably most other terrestrial organisms - carabid beetles are one of the most worthwhile model groups for biological studies.     

Using learning networks to understand complex systems: a case study of biological,geophysical and social research in the Amazon

Developing high‐quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini‐reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth‐atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub‐disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large‐scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions.     

The Oxford Dodo. Part 2: from curiosity to icon and its role in displays,education and research

The Tradescant or Oxford Dodo has played an important role in exhibition and education throughout its 360-year history, and has been the subject of scientific research reflecting changing interests and techniques over this time. Due to confusion over its relationships, its placement in the classification systems continually changed, until the dissection in 1847 of the head and foot confirmed its columbid (pigeons and doves) affinities. Here, we describe the dissection of the head and foot and the Tradescant Dodo’s display history, from the late nineteenth century until the present day, and also its use in education. We discuss the importance of the Tradescant Dodo to Lewis Carroll, whose ‘Alice’s Adventures in Wonderland’ made the dodo aware to a worldwide audience. We further provide an overview of recent work including electron microscopic study of feathers, mDNA analysis, cytological investigation of the skin and measuring of the brain capacity, all of which have added to our knowledge of the evolution and ecology of this most extraordinary of birds. Research is ongoing; the Tradescant Dodo is presently subject to CT scanning and functional analysis. This is the second part of a two-part paper.     

Short-term effects of air pollution,markers of endothelial activation,and coagulation to predict major adverse cardiovascular events in patients with acute coronary syndrome: insights from AIRACOS study

The aim of this study was to determine whether markers of inflammation and coagulation are associated with short-term particulate matter exposure and predict major adverse cardiovascular events at 360 d in patients with acute coronary syndrome (ACS). We included 307 consecutive patients, and assessed the average concentrations of data on atmospheric pollution in ambient air and meteorological variables from 1?d up to 7 d prior to admission. In patients with ACS, the markers of endothelial activation and coagulation, but not black carbon exposure, are associated with major adverse cardiovascular events at one-year follow-up.