The NemaGENETAG initiative: large scale transposon insertion gene-tagging in <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

The nematode Caenorhabditis elegans is a widely appreciated, powerful platform in which to study important biological mechanisms related to human health. More than 65% of human disease genes have homologues in the C. elegans genome, and essential aspects of mammalian cell biology, neurobiology and development are faithfully recapitulated in this organism. The EU-funded NemaGENETAG project was initiated with the aim to develop cutting-edge tools and resources that will facilitate modelling of human pathologies in C. elegans, and advance our understanding of animal development and physiology. The main objective of the project involves the generation and evaluation of a large collection of transposon-tagged mutants. In the process of achieving this objective the NemaGENETAG consortium also endeavours to optimize and automate existing transposon-mediated mutagenesis methodologies based on the Mos1 transposable element, in addition to developing alternatives using other transposon systems. The final product of this initiative—a comprehensive collection of transposon-tagged alleles—together with the acquisition of efficient transposon-based tools for mutagenesis and transgenesis in C. elegans, should yield a wealth of information on gene function, immediately relevant to key biological processes and to pharmaceutical research and development.     

Public and private mechanisms of life extension in <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Model organisms have been widely used to study the ageing phenomenon in order to learn about human ageing. Although the phylogenetic diversity between vertebrates and some of the most commonly used model systems could hardly be greater, several mechanisms of life extension are public (common characteristic in divergent species) and likely share a common ancestry. Dietary restriction, reduced IGF-signaling and, seemingly, reduced ROS-induced damage are the best known mechanisms for extending longevity in a variety of organisms. In this review, we summarize the knowledge of ageing in the nematode Caenorhabditis elegans and compare the mechanisms of life extension with knowledge from other model organisms.     

淡水入侵生物沼蛤的污损机制与防污措施研究进展

沼蛤是一种典型的淡水入侵贝类,能够利用其分泌的足丝牢固黏附在多种水下基质表面,引起严重的生物污损问题。沼蛤污损不但影响水生态系统健康,也给水利工程、交通运输、水产养殖等行业带来经济损失,已成为全球水生态系统安全和国民经济重要行业的潜在威胁,相关防污工作亟待开展。欲从根本上解决沼蛤污损问题,一方面需要加强对其基础生物学特性和污损机制的深入解析,另一方面也需要在此基础上研发更加经济、高效、环境友好的防污措施。本文综述了近年来国内外关于沼蛤污损生物学特性、污损机制和防污措施方面的研究进展,尤其是对沼蛤生物污损发生的主要机制如足探测识别、足丝黏附和环境影响等方面进行了总结,也从物理、化学、生物和防污材料等角度阐述了现有的沼蛤污损控制措施并对未来发展方向进行了展望,以期更加深入地理解沼蛤生物污损现象,为揭示其作用机制、制定科学有效的防污措施、维护水生态系统安全提供数据支撑,综述内容对于水下仿生材料研发也具有重要的参考价值。     

Regulation of vole populations by the nematode <Emphasis Type="Italic">Trichuris arvicolae</Emphasis>: insights from modelling

The goal of this study is to determine whether a parasitic nematode may regulate, or destabilise by inducing demographic cycles, its host populations. We explore three host–parasite systems through population dynamic models. The hosts considered are the fossorial water vole, Arvicola terrestris, the common vole Microtus arvalis and the bank vole Myodes (Clethrionomys) glareolus and the parasitic nematode is Trichuris arvicolae. Three differential equation-based mathematical models are developed including host immunity and the existence of trade-off between immunity and host survival. Using parameters estimated from field data and laboratory observations, all these models show that T. arvicolae can induce host population regulation but not demographic cycles. The regulation effect of the nematode is un-ambiguous for the water vole (reduction of 50.2% of the host population size), but less obvious for the common vole (5.9%) and even less for the bank vole (1.4%). Important biological parameters to be taken into account in such models are discussed. Experimental confirmation of the regulatory potential of the nematode and of the costs of mounting an immune response against this nematode are now required. Communicated by W. Lutz     

Bacteria associated with the pinewood nematode <Emphasis Type="Italic">Bursaphelenchus xylophilus</Emphasis> collected in Portugal

In this study, we report on the bacterial community associated with the pinewood nematode Bursaphelenchus xylophilus from symptomatic pine wilted trees, as well as from long-term preserved B. xylophilus laboratory collection specimens, emphasizing the close bacteria–nematode associations that may contribute to pine wilt disease development.     

Stability of entomopathogenic bacteria, <Emphasis Type="Italic">Xenorhabdus nematophila</Emphasis> and <Emphasis Type="Italic">Photorhabdus luminescens</Emphasis>, during in vitro culture

The entomopathogenic nematode–bacteria complexes Heterorhabditis bacteriophora/Photorhabdus luminescens and Steinernema carpocapsae/Xenorhabdus nematophila are mass produced for use as biological insecticides. Stability of the bacterial partner in culture is essential for maintaining traits important for both biological control and production. Two geographically distinct strains of each bacterial species were isolated from their nematode partners and serially subcultured on in vitro media to assess trait stability. Subculturing resulted in a shift to secondary cell production in one P. luminescens strain and both X. nematophila strains within ten in vitro culture cycles. However, when cell phenotypic variation was controlled in X. nematophila strains by regular selection for primary variants, no trait change was detected in the primary variant after prolonged subculture. When P. luminescens cell phenotypic variation was controlled by selection for primary variants, changes in the primary variant of both strains were noted including reductions in cell and inclusion body size and inclusion body prevalence. Bacterial ability to cause lethal infections following injection into the hemocoel of Tenebrio molitor larvae declined by more than half in primary variants of one P. luminescens strain. Conversely, yield was enhanced, with the subcultured P. luminescens strains showing 53.5 and 75.8% increases in primary cell density. Field adapted traits of primary variant P. luminescens strains tend to deteriorate during in vitro culture as tradeoffs for gains in yield. In vitro producers of the P. luminescens/H. bacteriophora complex must weigh the need for superior bacterial yield against the need to preserve traits important for biological control.     

A history of recent advancements on <Emphasis Type="Italic">Nephrops norvegicus</Emphasis> behavioral and physiological rhythms

Biological rhythms are a widespread feature of living organisms, being expressed at any level of their organization. Behavioral and physiological rhythms can affect the results on species stock assessment when the timing of sampling is not taken into account. That timing is of importance since animals may be present or not in a certain area of sampling depending on their activity cycle. As an example of this, the rhythmic behavior and physiology of one of the most commercially important European decapods, the Norway lobster (Nephrops norvegicus) was studied. These rhythms affect its commercial catchability at a diel and at a seasonal scale. Nephrops inhabits muddy bottoms where animals dig burrows that save them from the trawl tow capture when occupied. Catch patterns have been widely used as proxy of activity rhythms of populations of different depths. Catches show a modulation upon the day-night cycle since animals emerge under optimum environmental illumination in order to feed. Emergence is also affected in a not fully clarified manner by other variables of environmental and demographic nature (e.g. food presence, hunger state, sex, size, reproductive stage, territorialism and mating). All these features make Nephrops a good model of reference for studies on biological rhythms of other commercially important deep water decapods in relation to their ecological context. In this review, we summarize the actual knowledge on Nephrops behavioral and physiological rhythms. We will compare data obtained from laboratory tests on single individuals with data obtained from trawling of populations of different depths. We will also describe some new hypotheses on the rhythmic regulation of the species behaviour, as well as potential scenarios for future research.     

Differentially expressed genes in cotton plant genotypes infected with Meloidogyne incognita

Meloidogyne incognita is a nematode responsible for huge losses of economically important crops. The control of this pathogen is heavily centered on chemical nematicides, which are toxic to humans and environment, besides being very expensive. Alternatively, resistant varieties of cotton generated from conventional breeding programs represent an attractive strategy for the control of M. incognita. In this context, the goal of the work reported here was to analyze the gene expression profile of one resistant and one susceptible cotton genotype infected with M. incognita aiming to understand the mechanisms involved in resistance. EST libraries of cotton in both resistant and susceptible to infection by M. incognita were constructed and sequenced, generating 2261 sequences that were assembled into 233 contigs and 1593 singlets. Genes differentially expressed were observed in both resistant and susceptible cotton. Twenty genes were found to be expressed exclusively in the resistant cotton genotype, with functions related to pathogen recognition, signal transduction, defense mechanisms and protein synthesis transport and activation. The coordinated action of these genes suggests the existence of a complex defense pathway towards nematode attack in cotton. Our data indicate some candidate genes for validation and use through transformation in other agronomically important plants.     

Drosophila melanogaster as a model system for the study of the function of calcium/calmodulin-dependent protein kinase II in synaptic plasticity

Drosophila melanogaster has been used as a biological model system for almost a century. In the last several decades,Drosophila has been used as a system to probe the molecular basis of behavior and discoveries in the fly have been at the forefront of the elucidation of important basic mechanisms. This review will outline the variety of approaches that makeDrosophila an excellent model system with which to study the function of the enzyme calcium/calmodulin-dependent protein kinase II (CaMKII) in synaptic plasticity. CaMKII has a well documented role in behavior and synaptic plasticity in both vertebrates and invertebrates. The behavioral and genetic richness ofDrosophila allow for a multi-level approach to understanding the physiological roles of this enzyme's function.     

<Emphasis Type="Italic">CaMi</Emphasis>, a root-knot nematode resistance gene from hot pepper (<Emphasis Type="Italic">Capsium annuum</Emphasis> L.) confers nematode resistance in tomato

Several root-knot nematode (Meloidogyne spp.) resistance genes have been discovered in different pepper (Capsium annuum L.) lines; however, none of them has yet been cloned. In this study, a candidate root-knot nematode resistance gene (designated as CaMi) was isolated from the resistant pepper line PR 205 by degenerate PCR amplification combined with the RACE technique. Expression profiling analysis revealed that this gene was highly expressed in roots, leaves, and flowers and expressed at a lower level in stems and was not detectable in fruits. To verify the function of CaMi, a sense vector containing the genomic DNA spanning the full coding region of CaMi was constructed and transferred into root-knot nematode susceptible tomato plants. Sixteen transgenic plants carrying one to five copies of T-DNA inserts were generated from two nematode susceptible tomato cultivars. RT-PCR analysis revealed that the expression levels of CaMi gene varied in different transgenic plants. Nematode assays showed that the resistance to root-knot nematodes was significantly improved in some transgenic lines compared to untransformed susceptible plants, and that the resistance was inheritable. Ultrastructure analysis showed that nematodes led to the formation of galls or root knots in the susceptible lines while in the resistant transgenic plants, the CaMi gene triggered a hypersensitive response (HR) as well as many necrotic cells around nematodes. Rugang Chen and Hanxia Li are contributed equally to this work.     

Purification and characterization of a neutral serine protease with nematicidal activity from <Emphasis Type="Italic">Hirsutella rhossiliensis</Emphasis>

Serine protease plays an important role in fungal infection to invertebrate hosts. An extracellular protease (Hnsp) was detected in liquid culture of Hirsutella rhossiliensis OWVT-1 with nematodes (Panagrellus redivivus) as the unique nitrogen source and purified to homogeneity by ammonium sulphate precipitation, anion exchange chromatography and gel filtration. Its molecular mass was about 32 kDa, and the optimal reaction pH value and temperature were pH 7 and 40°C, respectively. The Hnsp activity was stable at pH 6–8 and decreased radically at 50°C for 10 min. Hnsp was highly sensitive to inhibitor of PMSF and well decomposed the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, suggesting that it belonged to the chymotrypsin/subtilisin of serine proteases. The N-terminal amino acid sequence of Hnsp was SVTDQQGADCGLARISHRE, which showed high homology with other serine proteases from nematophagous fungi. Ability to kill nematode and degrade its cuticle in vitro indicated that Hnsp could be involved in the infection of nematode.     

Environmental and industrial applications of Yarrowia lipolytica

Yarrowia lipolytica is a fungus that degrades hydrophobic substrates very efficiently. The fungus displays several important characteristics that have encouraged researchers to study various basic biological and biotechnological applications in detail. Although the organism has been used as model system for studying dimorphism, salt tolerance, heterologous protein expression, and lipid accumulation, there are no recent reviews on the environmental and industrial applications of this organism. Included here are applications in bioremediation of environments contaminated with aliphatic and aromatic compounds, organic pollutants, 2,4,6-trinitrotoluene, and metals. A variety of industrially important recent processes for the synthesis of β-hydroxy butyrate, l-dopa, and emulsifiers have also been reviewed. Production of unique inherent enzymes (inulinases, α-mannosidases), novel applications of esterases and lipases, and the use of the fungus for heterologous expression of biotechnologically relevant products have also been highlighted. The review while entailing a general overview focuses critically on some of the recent advances on the applications of this yeast. The examples cited here demonstrate the use of wild-type, mutant as well as genetically manipulated strains of Y. lipolytica for the development of different products, processes, and technologies. This also throws light on how a single organism can be versatile with respect to its metabolic abilities and how it can be exploited for a variety of purposes. This review will thus form a base for future developments in this field.     

锦鸡儿属灌丛化对草原化荒漠区土壤线虫群落组成和代谢足迹的影响

调查了内蒙古草原化荒漠区3种锦鸡儿[垫状锦鸡儿(Caragana tibetica)、荒漠锦鸡儿(C.roborovskyi)和狭叶锦鸡儿(C.stenophylla)]灌丛内、外土壤线虫群落多样性、组成和代谢足迹,以及相关的土壤理化性质和植物群落特征,旨在探讨锦鸡儿属灌丛对土壤线虫群落的影响,并分析这种影响是否具有灌木种间差异,同时从线虫功能团水平上探究灌丛如何通过非生物因素和生物因素影响线虫群落组成。结果表明：锦鸡儿属灌丛对土壤线虫多度、丰富度和多样性无显著影响,但却显著影响土壤线虫群落组成。原因是灌丛对土壤线虫群落具有物种选择性;灌丛可能主要是通过根系分泌物、凋落物质量等因素,而不是通过土壤理化性质和林下植物影响线虫群落组成。土壤线虫组成的变化引起线虫代谢足迹发生明显变化。灌丛内土壤线虫功能代谢足迹大于灌丛外(除狭叶锦鸡儿外),说明灌丛内土壤线虫群落对碳的利用率更高。3种锦鸡儿属灌木中,狭叶锦鸡儿的结构代谢足迹最大,表明狭叶锦鸡儿对捕食杂食类线虫代谢活性的促进作用更强。土壤线虫组成的变化通过线虫代谢足迹导致土壤食物网结构发生显著性变化。狭叶锦鸡儿灌丛土壤干扰程度低,营养富集状况好...     

Traditional Knowledge and Management of <Emphasis Type="Italic">Feijoa (Acca sellowiana)</Emphasis> in Southern Brazil

Traditional Knowledge and Management of Feijoa (Acca sellowiana) in Southern Brazil. This paper investigates traditional knowledge of the use and management of Acca sellowiana in southern Brazil. Fifty-six informants from three rural communities were assigned to one of four subgroups (“maintainers,” “managers,” “cultivators,” or “users”) based on their responses regarding management and use of A. sellowiana. Traditional knowledge related to use of this species is widespread among rural residents, but traditional knowledge related to management is fragmented depending on whether one uses, manages, or cultivates the species. Knowledge held in rural communities suggests that A. sellowiana could play an expanded role in local economies as well as biodiversity conservation. We suggest that participatory research could stimulate greater local use as well as on-farm conservation of A. sellowiana.     

<Emphasis Type="Italic">Bacillus subtilis</Emphasis> as a bioindicator for estimating pentachlorophenol toxicity and concentration

Pentachlorophenol (PCP) and its sodium salt (Na-PCP) are extremely toxic chemicals responsible for important soil and groundwater pollution, mainly caused by wastes from wood-treatment plants, because chlorinated phenols are widely used as wood preservatives. The methods most commonly used for routine analysis of pesticides such as PCP and Na-PCP are high-performance liquid chromatography (HPLC) and gas chromatography–mass spectroscopy (GC–MS). A variety of rapid biological screening tests using marine organisms, bioluminescent bacteria, and enzymes have also been reported. In this study, rapid biological screening analysis using Bacillus subtilis was developed, to assess the biodegradation of PCP and its by-products in liquid samples. An empirical model is proposed for spectrophotometric analysis of Na-PCP concentration after growth of Bacillus subtilis.     

Biological control potential of plant growth‐promoting rhizobacteria suppression of Meloidogyne incognita on cotton and Heterodera glycines on soybean: A review

Over the past decade, we have seen an increasing market for biopesticides and an increase in number of microbial control studies directed towards plant‐parasitic nematodes. This literature survey provides an overview of research on biological control of two economically important plant‐parasitic nematodes, Meloidogyne incognita (Kofoid & White) Chitwood (southern root‐knot nematode) and Heterodera glycines Ichinohe (soybean cyst nematode) using spore‐forming plant growth‐promoting rhizobacteria (PGPR). In this review, the current biological control strategies for the management of those cotton and soybean nematodes, the mechanism of using BacillusPGPR for biological control of plant‐parasitic nematode including induced systemic resistance and antagonism and the future of biological control agents on management of plant‐parasitic nematodes are covered.     

<Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> as an experimental tool for the study of complex neurological diseases: Parkinson’s disease,Alzheimer’s disease and autism spectrum disorder

The nematode Caenorhabditis elegans has a very well-defined and genetically tractable nervous system which offers an effective model to explore basic mechanistic pathways that might be underpin complex human neurological diseases. Here, the role C. elegans is playing in understanding two neurodegenerative conditions, Parkinson’s and Alzheimer’s disease (AD), and a complex neurological condition, autism, is used as an exemplar of the utility of this model system. C. elegans is an imperfect model of Parkinson’s disease because it lacks orthologues of the human disease-related genes PARK1 and LRRK2 which are linked to the autosomal dominant form of this disease. Despite this fact, the nematode is a good model because it allows transgenic expression of these human genes and the study of the impact on dopaminergic neurons in several genetic backgrounds and environmental conditions. For AD, C. elegans has orthologues of the amyloid precursor protein and both human presenilins, PS1 and PS2. In addition, many of the neurotoxic properties linked with Aβ amyloid and tau peptides can be studied in the nematode. Autism spectrum disorder is a complex neurodevelopmental disorder characterised by impairments in human social interaction, difficulties in communication, and restrictive and repetitive behaviours. Establishing C. elegans as a model for this complex behavioural disorder is difficult; however, abnormalities in neuronal synaptic communication are implicated in the aetiology of the disorder. Numerous studies have associated autism with mutations in several genes involved in excitatory and inhibitory synapses in the mammalian brain, including neuroligin, neurexin and shank, for which there are C. elegans orthologues. Thus, several molecular pathways and behavioural phenotypes in C. elegans have been related to autism. In general, the nematode offers a series of advantages that combined with knowledge from other animal models and human research, provides a powerful complementary experimental approach for understanding the molecular mechanisms and underlying aetiology of complex neurological diseases.     

Selection of insect parasitic nematodes for biological control of the garden chafer,Phyllopertha horticola

Larvae ofPhyllopertha horticola L. (Coleoptera: Scarabaeidae) cause increasing problems on sports fields and lawns in NW-Europe. A biological control programme using insect parasitic nematodes is being developed. This paper contains the results of bioassays with various species and isolates of the nematode generaHeterorhabditis andSteinernema. In bioassays in small pots with moist sand, most of the nematode isolates gave 30–60% mortality against each of the three larval stages. The susceptibility of the grubs for nematode infection generally increased with larval development.H. bacteriophora, H. heliothidis, H. megidis, a DutchHeterorhabditis isolate NLH-E87.3 andS. glaseri 326 showed the highest mortality rates, with nearly 100% mortality of third instar grubs. The DutchHeterorhabditis isolate NLH-E87.3 andS. glaseri 326 were selected as candidates for further studies on their potential as biological control agents forP. horticola grubs in the field.     

Investigation on the infection mechanism of the fungus <Emphasis Type="Italic">Clonostachys rosea</Emphasis> against nematodes using the green fluorescent protein

The fungus Clonostachys rosea (syn. Gliocladium roseum) is a potential biocontrol agent. It can suppress the sporulation of the plant pathogenic fungus Botrytis cinerea and kill pathogenic nematodes, but the process of nematode pathogenesis is poorly understood. To help understand the underlying mechanism, we constructed recombinant strains containing a plasmid with both the enhanced green fluorescent protein gene egfp and the hygromycin resistance gene hph. Expression of the green fluorescent protein (GFP) was monitored using fluorescence microscopy. Our observations reveal that the pathogenesis started from the adherence of conidia to nematode cuticle for germination, followed by the penetration of germ tubes into the nematode body and subsequent death and degradation of the nematodes. These are the first findings on the infection process of the fungal pathogen marked with GFP, and the developed method can become an important tool for studying the molecular mechanisms of nematode infection by C. rosea. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Lin Zhang and Jinkui Yang contributed equally to this work.     

Soil microorganisms control plant ectoparasitic nematodes in natural coastal foredunes

Belowground herbivores can exert important controls on the composition of natural plant communities. Until now, relatively few studies have investigated which factors may control the abundance of belowground herbivores. In Dutch coastal foredunes, the root-feeding nematode Tylenchorhynchus ventralis is capable of reducing the performance of the dominant grass Ammophila arenaria (Marram grass). However, field surveys show that populations of this nematode usually are controlled to nondamaging densities, but the control mechanism is unknown. In the present study, we first established that T. ventralis populations are top-down controlled by soil biota. Then, selective removal of soil fauna suggested that soil microorganisms play an important role in controlling T. ventralis. This result was confirmed by an experiment where selective inoculation of microarthropods, nematodes and microbes together with T. ventralis into sterilized dune soil resulted in nematode control when microbes were present. Adding nematodes had some effect, whereas microarthropods did not have a significant effect on T. ventralis. Our results have important implications for the appreciation of herbivore controls in natural soils. Soil food web models assume that herbivorous nematodes are controlled by predaceous invertebrates, whereas many biological control studies focus on managing nematode abundance by soil microorganisms. We propose that soil microorganisms play a more important role than do carnivorous soil invertebrates in the top-down control of herbivorous ectoparasitic nematodes in natural ecosystems. This is opposite to many studies on factors controlling root-feeding insects, which are supposed to be controlled by carnivorous invertebrates, parasitoids, or entomopathogenic nematodes. Our conclusion is that the ectoparasitic nematode T. ventralis is potentially able to limit productivity of the dune grass A. arenaria but that soil organisms, mostly microorganisms, usually prevent the development of growth-reducing population densities.