Remote European mountain lake ecosystems: regionalisation and ecological status

1. A survey of c. 350 remote high altitude and high latitude lakes from 12 different mountain regions across Europe was undertaken to explore ecosystem variability, climate forcing, environmental conditions and pollution threats at a scale not previously attempted.
2. Lakes were sampled for a range of contemporary and sub-fossil organisms including planktonic crustaceans, rotifers, littoral invertebrates, chironomids, diatoms and cladocerans. Survey and cartographic data were used to determine environmental characteristics at each site. Organic pollutants and trace metal concentrations were measured in the lake sediment.
3. A number of separate studies were undertaken which examined the environmental characteristics of the surveyed lakes (climate forcing and chemical composition), distribution of biota relative to local, regional and biogeographical factors and pollution threats (acidification, heavy metals and persistent organic pollutants) to these sensitive ecosystems.
4. There is a strong regional element to the way that environmental factors combine (including climate and pollution threats) and the biota responds in mountain lakes across Europe. From a management perspective it is clear that lake classification and the development of useful typologies and assessments of reference conditions should be undertaken at regional rather than pan-European scales.
5. There are some common features across lake districts related to the timing of industrialisation, but the studies carried out on metals, organic pollutants and nitrate deposition indicate that each lake district has distinct pollution threats. Climate warming already affects most of the lake districts and there are considerable uncertainties as to how this will modify conditions in remote European mountain systems.
6. The lake district concept goes beyond a geographical construct and merits further theoretical and experimental development as an ecological concept.     

Electrophysiology and glaucoma: current status and future challenges

Visual electrophysiology allows non-invasive monitoring of the function of most processing stages along the visual pathway. Here, we consider which of the available methods provides the most information concerning glaucomatous optic nerve disease. The multifocal electroretinogram (ERG), although often employed, is less affected in glaucoma than two direct measurements of retinal ganglion cell function, namely the pattern ERG (PERG) and the photopic negative response (PhNR) of the ERG. For the PERG, longitudinal studies have been reported, suggesting that this method can be used for the early detection of glaucoma; for the PhNR, no longitudinal study is available as yet. The multifocal PERG can spatially resolve ganglion cell function but its glaucomatous reduction is typically panretinal, even with only local field changes and so, its topographic resolution is of no advantage in glaucoma. The multifocal visual evoked potential promises objective perimetry and shows sensitivity and specificity comparable with standard automated perimetry but has not been established as a routine tool to date.     

Long-term dynamics of Collembolan populations in forest and meadow ecosystems

The population dynamics of soil-dwelling springtails in a spruce forest (Piceetum oxalidosum) and a dry meadow with young planted spruce trees was analyzed based on an eight-year sampling in Moscow Region. Fluctuations of population densities of the most species are less than 10 fold. The seasonal dynamics (the number and position of peaks) is more constant in surface-dwelling species than in hemi-and euedaphic ones. The occurrence of the density peaks in specific seasons is merely a tendency. Two types of the size structure of populations are revealed: the “left-sided” type with prevalence of small immature individuals and the “symmetrical” one with prevalence of medium-sized individuals. Synchronization of reproduction in the species studied is possible only under the effect of external climatic factors. The seasonal density dynamics of most abundant species is related to the temperature and, to a lesser extent, precipitation. The mean density of some species in the following year can be predicted based on the mean temperature and/or sum of precipitation in the current year. In the forest, the density-dependent regulation of springtail abundance is probable. The springtail populations do not respond to overgrowing of the meadow with spruce trees at least at the beginning of this process.     

Prokaryote diversity and taxonomy: current status and future challenges

The prokaryotes are by far the most abundant organisms inhabiting planet Earth. They are also by far the most diverse, both metabolically and phylogenetically; they encompass the Bacteria and the Archaea, two out of the three major divisions of living organisms. The current prokaryote species classification is based on a combination of genomic and phenotypic properties. The recommended cut-off value of 70% DNA-DNA similarity to delineate species signifies an extremely broad species definition for the prokaryotes compared with the higher eukaryotes. The number of validly named species of prokaryotes is currently slightly more than 6200. However, on the basis of small-subunit rDNA characterization of whole communities and other approaches, the more exact number of species present can be inferred to be at least two orders of magnitude larger. Classic culturing methods based on colony formation on agar are generally unsatisfactory for the recovery of bacteria from the environment. Many of the most abundant prokaryotes in nature have not yet been brought into culture. Some of these may thrive by means of as yet unknown modes of energy generation. Several novel methods have recently enabled the isolation of some interesting organisms of environmental significance. A better coverage of the prokaryote diversity on Earth depends on such innovative approaches, combined with appropriate funding.     

Evolution and current status of ecological phytochemistry

Phytochemical studies have experienced a great deal of change during the last century, not only regarding the number of compounds described, but also in the concept of phytochemistry itself. This change has mainly been related to two key points: the methodologies used in phytochemical studies and the questions regarding 'why secondary metabolites appeared in plants and in other living organisms?' and 'what is their role?'. This transformation in the field has led to new questions concerning such different subjects as evolution, paleobotany, biochemistry, plant physiology and ethnography. However, the main issue is to clarify the role that secondary metabolites play in the plant (and other organisms) and whether the resources invested in their production (C and N allocation, genes encoding their biogenetic pathways, specific enzymes, energy-rich molecules such as ATP and NADPH) have or lack a reasonable reward in terms of advantages for survival. Consequently, in this review the main emphasis will be placed on two subjects related to the evolution of phytochemical studies. The first aim is to describe briefly the influence that the development of the methodologies needed for compound isolation and structure elucidation have had on the field of phytochemistry. The second area to be covered concerns the new theories addressing the role of secondary metabolites from an ecological point of view: co-evolution of plants and their potential enemies (phytophagous insects, microbes, herbivores and other plants), chemical plant defence, adaptative strategies of phytophagues to plant toxins (among them sequestration will be briefly mentioned), and models and theories for carbon and nitrogen allocation. Some final remarks are made to summarize our opinion about the immediate future of phytochemical ecology and phytochemical studies.     

Mammary gland stem cells: current status and future challenges

Distinct subsets of cells, including cells with stem cell-like properties, have been proposed to exist in normal human breast epithelium and breast carcinomas. The cellular origins of epithelial cells contributing to gland development, tissue homeostasis and cancer are, however, still poorly understood. The mouse is a widely used model of mammary gland development, both directly by studying the mouse mammary epithelial cells themselves and indirectly, by studying development, morphogenesis, differentiation and carcinogenesis of xenotransplanted human breast epithelium in vivo. While in early studies, human or mouse epithelium was implanted as fragments into the mouse gland, more recent technical progress has allowed the self-renewal capacity and differentiation potential of distinct cell populations or even individual cells to be interrogated. Here, we review and discuss similarities and differences between mouse and human gland development with particular emphasis on the identity and localization of stem cells, and the influence of the surrounding microenvironment. It is concluded that while recent advances in the field have contributed immense insight into how the normal mammary gland develops and is maintained, significant discrepancies exist between the mouse and human gland which should be taken into consideration in current and future models of mammary stem cell biology.     

Taxonomy of halophilic Archaea: current status and future challenges

Several groups of Archaea, all Euryarchaeota, develop in hypersaline environments (from >10 % salt up to saturation). The cultured diversity of halophilic Archaea includes the family Halobacteriaceae of aerobic or facultative anaerobic, generally red-pigmented species (47 genera and 165 species as of February 2014) and seven representatives of four genera of methanogens, most of which obtain energy from methylated amines under anaerobic conditions. Metagenomic studies have identified an additional deep lineage of Archaea in salt lakes and ponds with brines approaching NaCl saturation. Genomic information is now available for representatives of these ‘Nanohaloarchaea’, but no members of this lineage have yet been cultured. Multilocus sequence analysis is becoming increasingly popular in taxonomic studies of the Halobacteriaceae, and such studies have demonstrated that recombination of genetic traits occurs at an extremely high frequency at least in some genera. Metagenomic studies in an Antarctic lake showed that large identical regions of up to 35 kb in length can be shared by members of different genera living together in the same environment. Such observations have important implications not only for the taxonomy of the Halobacteriaceae, but also for species concepts and questions on taxonomy and classification for prokaryotic microorganisms in general.     

Genetic transformation of fruit trees: current status and remaining challenges

Genetic transformation has emerged as a powerful tool for genetic improvement of fruit trees hindered by their reproductive biology and their high levels of heterozygosity. For years, genetic engineering of fruit trees has focussed principally on enhancing disease resistance (against viruses, fungi, and bacteria), although there are few examples of field cultivation and commercial application of these transgenic plants. In addition, over the years much work has been performed to enhance abiotic stress tolerance, to induce modifications of plant growth and habit, to produce marker-free transgenic plants and to improve fruit quality by modification of genes that are crucially important in the production of specific plant components. Recently, with the release of several genome sequences, studies of functional genomics are becoming increasingly important: by modification (overexpression or silencing) of genes involved in the production of specific plant components is possible to uncover regulatory mechanisms associated with the biosynthesis and catabolism of metabolites in plants. This review focuses on the main advances, in recent years, in genetic transformation of the most important species of fruit trees, devoting particular attention to functional genomics approaches and possible future challenges of genetic engineering for these species in the post-genomic era.     

PEG-modified carbon nanotubes in biomedicine: current status and challenges ahead

Since their discovery at the end of the previous millennium, carbon nanotubes (CNTs) have been the object of thousands of papers describing their applications in fields ranging from physics to electronics, photonics, chemistry, biology, and medicine. The development of chemical approaches to modify their graphitic sidewalls enabled the generation of poly(ethylene glycol) (PEG)-modified CNTs and their exploration in multiple biomedical applications. Studies at the cellular and organism level revealed that PEG-modified CNTs have favorable pharmacokinetic and toxicology profiles. Recently, PEG-modified CNTs have been successfully tested in preclinical studies in the fields of oncology, neurology, vaccination, and imaging, suggesting that they are well suited for the generation of novel multifunctional nanodrugs. Here we will review published data about the application of PEG-modified CNTs as in vitro and in vivo therapeutic and imaging tools and describe what is known about the interaction between PEG-modified CNTs and biological systems. Although several pieces of the puzzle are still missing, we will also attempt to formulate a preliminary structure-function model for PEG-modified CNT cellular trafficking, disposition, and side effects.     

Management of the natural ecosystems of the Cape Peninsula: current status and future prospects

The Cape Peninsula is an area of outstanding natural beauty and exceptional biodiversity, worthy of proclamation as a World Heritage Site. The area is dominated by fynbos vegetation, usually managed by means of prescribed burning, together with various programmes aimed at the control of invasive alien plant species. Effective management of the Peninsula is bedevilled by the fact that the area is controlled by no less than 14 different public bodies, resulting in fragmentation of effort and the lack of a standardized approach to management. Historically, many official and unofficial investigations have called for this problem to be resolved, without success. The lack of coherent, focused, and well funded fire and alien weed control management plans for the entire Peninsula is a serious deficiency. Despite this, considerable progress has been made towards the establishment of a database for the Peninsula, and the development of decision support systems that can utilize this database for rational management. Adoption of such a system would provide a powerful uniting tramework that would standardize and influence the management approaches adopted by the various controlling authorities.     

Phytoplankton and ecological status of forest lakes in the Omsk Priirtyshye

According to the materials of multiyear studies, the author estimates the ecological status of forest lakes in the Omsk Priirtyshye with respect to the phytoplankton development indicators. The species composition, structure, and floristic similarity degree of the phytoplankton of polytypic forest lakes are described. The author also determines the trophic status and water quality of these lakes. It is found that excessive recreation has a negative impact on the ecological status of the lakes.     

Arboreal tropical forest vertebrates: current knowledge and research trends

We review the ecology and specialized methods required for studying arboreal mammals, birds, reptiles and amphibians, and use faunal checklists from 12 tropical wet forest sites and an analysis of all articles published during the past ten years in 14 major journals to assess current knowledge and general research trends for these groups. The percentage of arboreal vertebrates was remarkably similar at the different sites (76.2 ± 3.9%). Birds were the most arboreal group and amphibians and reptiles the least. The review of journals showed that primates were overwhelmingly the most studied group (336 papers), followed by bats (105), passeriform birds (73) and rodents (55). Judging by their portion of the arboreal vertebrate community and the number of papers surveyed, birds and amphibians and reptiles are vastly understudied compared to mammals, but this is largely due to the great number of primate studies. The number of publications on arboreal vertebrates has remained relatively stable over the last 10 years for all taxa except primates, which have seen a growth in publications. Canopy vertebrates from Brazil had by far the most publications (120), followed by Madagascar (61), Costa Rica (55) and Indonesia (42). We conclude by highlighting the priorities we see for future studies on tropical canopy vertebrates.     

Plant proteomics in India and Nepal: current status and challenges ahead

Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.     

Trends in shark bycatch research: current status and research needs

Over the last few decades, much effort has been devoted towards quantifying and reducing bycatch in marine fisheries. Of late, there has been a particular focus on sharks given that bycatch is a frequently listed threat for sharks on the International Union for the Conservation of Nature Red List. However, currently there are no quantitative reviews or syntheses that explore the issue of shark bycatch globally which is problematic given that such a synthesis could inform conservation actions and identify pressing research gaps. We performed a qualitative and quantitative survey of the peer-reviewed literature to characterize trends in shark bycatch research with a particular goal of identifying research needs and opportunities. Using a structured literature review we identified 103 papers that met our search criteria, with the first one published in 1993. Early research efforts focused on documenting the scope of bycatch (i.e., determining that sharks were indeed captured as bycatch), but more recently there have been increased efforts devoted to developing and evaluating bycatch reduction strategies for sharks. Research activity was most common in the North Atlantic (~40?% of the total articles analysed) with comparatively less research in other areas such as the Indo-Pacific region where shark bycatch is regarded as particularly common and problematic. Most studies were observational with comparatively fewer experimental and modeling studies, and even fewer that combined research approaches. Gear modifications (e.g., hook size and type for long lines, net size and mesh design for nets) were the most commonly evaluated strategy for reducing shark bycatch; however, development and use of techniques like repellents, or seasonal area closures, or a combination of strategies, offer interesting possibilities that require further study. In addition, although many sharks are discarded, little is known about post-release survival or sub-lethal consequences of fisheries interactions, or evaluations of different fish handling strategies, making it difficult to quantify the true cost of bycatch or to recommend handling strategies to fishers. Although there are some inherent challenges with developing and testing shark bycatch reduction strategies, there is an urgent need to do so and this would be best achieved through interdisciplinary research that spans field, laboratory, and modeling realms.     

Plants in the forest canopy: some reflections on current research and future direction

Plants are one of the sessile components of the forest canopy, and consequently quantitative studies of plant components are more widely available than for some of their mobile counterparts. From a global perspective, several exciting and innovative canopy access tools have been designed over the past few decades that have facilitated the expansion our understanding of canopy plants. These include a network of canopy cranes, the development of the French luge (or sled), and the construction of walkways and platforms for access into different levels of the canopy on a permanent basis. At the recent international forest canopy conference in Sarasota, Florida (Forest Canopies 1998: Global Perspectives, November 4–8, 1998), many canopy plant studies were presented that illustrated the achievements in this field. As co-chair at this event, I present here some reflections based on my observations of the development of canopy research between the first and second international conferences. A selection of case studies from the conference presentations are cited in this review, including: tree crown respiration studies from the crane in Panama; epiphyte ecology from walkways in Peru; insect-plant relationships in tree crowns of the USA using platforms; experimental studies of epiphytes in cloud forests using single rope techniques; and epiphyte diversity surveys in Africa. Ideas for the future are also mentioned such as the novel concept of canopy farming of orchids in Costa Rica, the linking of canopy processes to forest floor activities, and the construction of canopy walkways to provide a sustainable forest economy instead of the conventional practice of logging. The integration of research with sustainable use of forests provides a conservation theme for future canopy studies. Such new approaches to studies of canopy plants are important, as scientists increasingly play a role in global conservation policies.     

Saliva proteome research: current status and future outlook

Human saliva harbours proteins of clinical relevance and about 30% of blood proteins are also present in saliva. This highlights that saliva can be used for clinical applications just as urine or blood. However, the translation of salivary biomarker discoveries into clinical settings is hampered by the dynamics and complexity of the salivary proteome. This review focuses on the current status of technological developments and achievements relating to approaches for unravelling the human salivary proteome. We discuss the dynamics of the salivary proteome, as well as the importance of sample preparation and processing techniques and their influence on downstream protein applications; post-translational modifications of salivary proteome and protein: protein interactions. In addition, we describe possible enrichment strategies for discerning post-translational modifications of salivary proteins, the potential utility of selected-reaction-monitoring techniques for biomarker discovery and validation, limitations to proteomics and the biomarker challenge and future perspectives. In summary, we provide recommendations for practical saliva sampling, processing and storage conditions to increase the quality of future studies in an emerging field of saliva clinical proteomics. We propose that the advent of technologies allowing sensitive and high throughput proteome-wide analyses, coupled to well-controlled study design, will allow saliva to enter clinical practice as an alternative to blood-based methods due to its simplistic nature of sampling, non-invasiveness, easy of collection and multiple collections by untrained professionals and cost-effective advantages.