A review of the research on introduced freshwater fishes: new perspectives,the need for research,and management implications

Although freshwater fishes have a long history of human-induced introduction, recent globalization has accelerated worldwide introduction events even more, and those introduced fish species are now perceived to be a major threat to ecosystems. Over the last two decades, numerous studies have been published on introduced fish species; however, it has been challenging for researchers to understand the magnitude of the impact and the underlying mechanism of invasions. Recently, new perspectives in understanding invasive freshwater fish biology have been presented in a number of studies, which can be largely attributed to advances in analytical techniques and also to a growing need for proactive analysis in management strategies. The aim of this paper is to summarize new ecological perspectives, the need for research, and/or management implications with emphasis on technological advances in, for example, statistics, molecular analysis, modeling techniques, and landscape analysis addressed under the following five categories: introduction pathways, predicting spatial patterns, biotic homogenization, hybridization, and control and eradication. The conservation of native fish fauna and the management of introduced fish species will benefit from combining these new perspectives with fundamental studies such as those on life history and population biology.     

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.     

Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research

The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields.     

Methodological Reflections on the Use of Remote Sensing and Geographic Information Science in Human Ecological Research

Environmental analysts increasingly utilize remote sensing (RS) and geographic information science (GIS) techniques to study the relationship between human societies and their biophysical environment. This paper considers the influence these techniques have had on environmental research. Using the case of the Sahel, the paper first relates contemporary applications of RS/GIS to the history of the environmental scientific practice in the region. While facilitating an expansion of spatiotemporal scales, applications of these new techniques continue the methodological failings of the past by relying on visual measures of environmental change and problematic indicators of human land-use pressures. The human ecology fields (human, cultural, and political ecologies), by emphasizing the causal connections between local management and environmental change, can address the problems inherent with the spatial analytical turn in environmental science. Using the author's experience with the use of GIS in a political ecology study of grazing management in western Niger, ways of more closely integrating RS/GIS techniques into human ecological research are discussed.     

Impact of fungal molecular genetics on biotechnology

Summary The application of biotechnology has a very long history and life has benefited a lot from the application of fungal products. The industrial successful application of the use of fungi has been due to pioneering activities in both universities and industry. The most recent example of the application of a new technique was demonstrated with recombinant DNA techniques. Until now these techniques were mainly applied to rather simple processes. But we might also expect in the near future the application of these techniques to more complex systems. A very interesting area in this respect might be the production of plant secondary metabolites by fungi. As far as the economic benefits are concerned, a good balance has to be found between the economics of the processes and constrains posed on these processes by governmental regulations.     

A history of the study of solid tumour growth: The contribution of mathematical modelling

A miscellany of new strategies, experimental techniques and theoretical approaches are emerging in the ongoing battle against cancer. Nevertheless, as new, ground-breaking discoveries relating to many and diverse areas of cancer research are made, scientists often have recourse to mathematical modelling in order to elucidate and interpret these experimental findings. Indeed, experimentalists and clinicians alike are becoming increasingly aware of the possibilities afforded by mathematical modelling, recognising that current medical techniques and experimental approaches are often unable to distinguish between various possible mechanisms underlying important aspects of tumour development. This short treatise presents a concise history of the study of solid tumour growth, illustrating the development of mathematical approaches from the early decades of the twentieth century to the present time. Most importantly these mathematical investigations are interwoven with the associated experimental work, showing the crucial relationship between experimental and theoretical approaches, which together have moulded our understanding of tumour growth and contributed to current anti-cancer treatments. Thus, a selection of mathematical publications, including the influential theoretical studies by Burton, Greenspan, Liotta et al., McElwain and co-workers, Adam and Maggelakis, and Byrne and co-workers are juxtaposed with the seminal experimental findings of Gray et al. on oxygenation and radio-sensitivity, Folkman on angiogenesis, Dorie et al. on cell migration and a wide variety of other crucial discoveries. In this way the development of this field of research through the interactions of these different approaches is illuminated, demonstrating the origins of our current understanding of the disease.     

Opportunities for synthetic plant chimeral breeding: Past and future

Many plant periclinal chimeras are selected by horticulturalists due to their distinctive, valuable phenotypes, and because they are relatively stable. Most of these have arisen by induced or spontaneous mutation. Interspecific chimeras have been accidentally produced from graft unions of plants from a wide range of families. Early last century Winkler developed a technique to produce interspecific chimeras from graft unions (graft chimeras). More recently in vitro techniques have been developed to synthesize interspecific and intervarietal chimeras. However, these techniques have only been successful for species in the families Solanaceae and Cruciferae, and rarely assessed on plants in other families. Research is required to improve these techniques or develop new approaches so that the efficiency of chimeral shoot production is improved and the techniques are applicable to plants in a wide range of families. The unique characteristics of interspecific or intervarietal chimeras show the potential of chimeral breeding to produce new cultivars. If chimeral breeding techniques were improved, they could become a standard breeding approach for some horticultural crops.     

Evolution and adaptive radiation of antarctic fishes

There are few instances where a knowledge of the thermal physiology, habitats and lifestyles of a group of closely related species can be mapped onto a well-supported phylogeny and a detailed climatic history. The unique fish fauna of the Southern Ocean, dominated by a single group of fish whose phylogeny is known from traditional and molecular techniques, provides one such opportunity. Furthermore, these fish are living at an extreme temperature for marine organisms. Physiological and molecular studies are revealing details of the mechanisms of temperature compensation and, combined with knowledge of the thermal history, are throwing new light on the process of evolution in this unique group of fish.     

New media and the digitized paranormal: instrumentation,affective atmospheres,and the production of history in Chile

In the last decade in Chile, an increasing amount of paranormal investigation companies have carried out ghost tours in patrimonial and historical places, using diverse technologies to penetrate into the history of sites. We ethnographically and analytically explore two related questions. First, we ask what paranormal instrumentation does to collective memory and to history. We argue that these ‘registers’ of the paranormal create ‘affective atmospheres’, namely from the forms of indeterminacy embedded in the functioning and performance of the apparatuses. Our argument is that these machines are mechanisms for the creation of a new history, one that is apprehended affectively. Second, in the context of an explosion of adherence in Chile to forms of new media, we employ the notion of ‘dark media’ to illustrate that online material posted by paranormal researchers appears to escape any form of mediational understanding, feeding at once the public's perceptive and affective dispositions.     

Genome complexity of harmful microalgae

During the past decade, next generation sequencing (NGS) technologies have provided new insights into the diversity, dynamics, and metabolic pathways of natural microbial communities. But, these new techniques face challenges related to the genome size and level of genome complexity of the species under investigation. Moreover, the coverage depth and the short-read length achieved by NGS based approaches also represent a major challenge for assembly. These factors could limit the use of these high-throughput sequencing methods for species lacking a reference genome and characterized by a high level of complexity. In the present work, the evolutionary history, mainly consisting of gene transfer events from bacteria and unicellular eukaryotes to microalgae, including harmful species, is discussed and reviewed as it relates to NGS application in microbial communities, with a particular focus on harmful algal bloom species and dinoflagellates. In the context of genetic population studies, genotyping-by-sequencing (GBS), an NGS based approach, could be used for the discovery and analysis of single nucleotide polymorphisms (SNPs). The NGS technologies are still relatively new and require further improvement. Specifically, there is a need to develop and standardize tools and approaches to handle large data sets, which have to be used for the majority of HAB species characterized by evolutionary highly dynamic genomes.     

Paleo-parasitology and the antiquity of human host-parasite relationships

Paleo-parasitology may be developed as a new tool to parasite evolution studies. DNA sequences dated thousand years ago, recovered from archaeological material, means the possibility to study parasite-host relationship coevolution through time. Together with tracing parasite-host dispersion throughout the continents, paleo-parasitology points to the interesting field of evolution at the molecular level. In this paper a brief history of paleo-parasitology is traced, pointing to the new perspectives opened by the recent techniques introduced.     

旧石器时代遗址发掘与记录方法讨论

随着技术的发展和研究理念的转变,旧石器时代考古遗址的发掘和记录方法也发生着变化。20世纪30年代周口店遗址发掘方法的改革是中国旧石器时代考古发掘史上的重大转折,奠定了中国旧石器时代考古发掘、记录方法的基础。90年代,中美联合考古在泥河湾地区的开展使中国旧石器时代考古遗址的发掘和记录方法与国际接轨,更加规范化、科学化。进入21世纪,新技术、新理念的应用使旧石器时代考古遗址发掘的记录方法更加多样化、提取的遗存信息更加科学化、综合化。本文以周口店遗址和泥河湾盆地旧石器时代遗址的发掘历史为主线,简要回顾旧石器时代考古发掘记录方法的变革;以东谷坨遗址的新发掘为例,介绍该遗址发掘和记录的一般规则和具体方法,呼吁建立具有科学性和包容性的旧石器时代遗址考古发掘操作规程。     

Native oak chloroplasts reveal an ancient divide across Europe

Glacial refugia and postglacial migration are major factors responsible for the present patterns of genetic variation we see in natural populations. Traditionally postglacial history has been inferred from fossil data, but new molecular techniques permit historical information to be gleaned from present populations. The chloroplast tRNA^Leu1 intron contains regions which have been highly conserved over a billion years of chloroplast evolution. Surprisingly, in one of these regions which has remained invariant for all photosynthetic organisms so far studied, we have found intraspecific site polymorphism. This polymorphism occurs in two European oaks, Quercus robur and Q. petraea , indicating hybridisation and introgression between them. Two distinct chloroplast types occur and are distributed geographically as eastern and western forms suggesting that these oaks are each derived from at least two separate glacial refugia.     

Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens

Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and MDIV). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (theta), population divergence time (t), and time to the most recent common ancestor (TMRCA) from MDIV were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.     

The anatomy of the greater occipital nerve: implications for the etiology of migraine headaches

An interest in pursuing new theories of the underlying etiology of migraine headaches has been sparked by previously published reports of an association between amelioration of migraine headache symptoms and corrugator resection during endoscopic brow lift. This theory has further been reinforced by recent publications documenting improvement in migraine headaches following injection of botulinum A toxin. There are thought to be four major "trigger points" along the course of several peripheral nerves that may cause migraine headaches. Among these peripheral nerves is the greater occipital nerve. For this reason, the authors have undertaken an anatomic study of this nerve to determine its usual course, potential anatomic variations, and possible points of potential entrapment or compression. The results of this anatomic study have enhanced further development of techniques designed to address these points of entrapment/compression and potentially lead to relief of migraine headaches caused by this mechanism. Twenty cadaver heads from patients with an unknown history of migraine headaches were dissected to trace the normal course of the greater occipital nerve from the semispinalis muscle penetration to the superior nuchal line. Standardized measurements were performed on 14 specimens to determine the location of the emergence of the nerve using the midline and occipital protuberance as landmarks. On the basis of this information, the location of emergence was determined to be at a point centered approximately 3 cm below the occipital protuberance and 1.5 cm lateral to the midline. This location can, in turn, be used to guide the practitioner performing chemodenervation of the semispinalis capitis muscle in an attempt to provide migraine symptom relief.     

Interpretation of variation across marker loci as evidence of selection

Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also have been strongly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responded to selection during the divergence of populations, then we may obtain better estimates of the parameters of population history by excluding these loci. Previous attempts were made to identify outlier loci from the distribution of sample statistics under neutral models of population structure and history. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and construct sample statistics that are estimators of these parameters. We then use the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus. This is so because the conditional distribution is less sensitive to the values of nuisance parameters.     

Wind tunnel evaluation of several tracer and collection techniques for the measurement of spray drift

In the history of pesticide drift measuring techniques, different tracers and a lot of different collection techniques have been used. At the start of a new Flemish project 'Protecting the Flemish environment against drift - The importance of drift-reducing techniques', wind tunnel tests have been executed to select the most efficient tracer and collection technique. As tracer types a fluorescent tracer Renaissance W15, 2 different chelates, a NaCl-solution and a fungicide Tolylfluanide were used. 2 different collection techniques were tested: drains incorporated in the wind tunnel floor filled with filter paper and filled with cloths. The recovery of the different tracers combined with the 2 collection materials was calculated. The advantages and disadvantages of the tracers and collection materials are enumerated in this article.     

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.