The changing epitome of species identification – DNA barcoding

The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The ‘DNA barcodes’ show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.     

Is changing hypothalamic activity important for control of ovulation?

The activity of the hypothalamic gonadotrophin releasing hormone pulse generator in women with regular ovulatory and anovulatory menstrual cycles was assessed to see whether changes therein are important determinants of normal and impaired ovarian function. Endogenous gonadotrophin releasing hormone secretion was inferred by measurement of the pituitary luteinising hormone response by characterisation of pulsatile luteinising hormone release over eight hours on three occasions during the course of follicular development and once during the luteal stage of the same cycles. In 13 ovulatory cycles (serum progesterone concentration greater than 25 nmol/l) confirmed by ovarian ultrasonography a pronounced variability in luteinising hormone pulse patterns among subjects was compatible with ovulation. In the luteal stage of ovulatory cycles the luteinising hormone interpeak interval (85 min, range 42-125) was significantly longer than that during the early follicular (64 min, 40-103), mid-follicular (62 min, 37-107), and late follicular (59 min, 39-80) stages of the same cycles. Thus in ovulatory cycles no increase in frequency of the gonadotrophin releasing hormone pulse generator was detected during follicular development, though this activity decreased in the luteal stage. In five late follicular stage studies in which part of the preovulatory luteinising hormone surge was captured no change in pulse frequency of luteinising hormone was detected compared with the mid-follicular stage of the same cycles or when compared with the late follicular stage of other cycles when no luteinising hormone surge was captured. Though mean luteinising hormone concentrations in luteinising hormone surge series (36 IU/l) were high, the amplitude of luteinising hormone pulses (165%) was only slightly greater than during non-surge late follicular stage studies (145%). Hence no change in hypothalamic gonadotrophin releasing hormone activity is required to generate the preovulatory discharge of luteinising hormone in man, which occurs as a result of the sensitising action of rising oestradiol concentrations on pituitary responsiveness to the same hypothalamic input signal. Luteinising hormone pulse frequency, peak amplitude, and mean serum luteinising hormone concentrations in seven anovulatory cycles (progesterone concentration less than 10 nmol/l) were not different from those at comparable stages of ovulatory cycles. These data suggest that the primary abnormality in this group of regularly menstruating anovulatory women lies in the ovary rather than in the hypothalamic control of the anterior pituitary.     

A comment on “Changing estuaries,changing views”

The provision of flood safety is of paramount importance in densely populated deltaic regions. The Dutch rely on flood defences to protect their lives and livelihoods from large-scale floods. The paper “Changing estuaries, changing views” (Smits et al., Hydrobiologica 565:339–355, 2006) criticizes this strategy and presents an alternative that could be summarized as a proposal to leave deltas untouched and to rely on natural sedimentation to reduce the impact of floods. It seems questionable, however, whether such a strategy will often be compatible with population pressures and efforts to stimulate economic growth. Moreover, it presupposes morphological conditions that seem highly unrealistic, not just in the Netherlands but also in many other sediment-starved coastal systems. Other than recommending countries not to implement the Dutch flood protection strategy and to leave deltas untouched, it should be recommended that solutions be tailored to local circumstances. The choice of a flood protection strategy should be based on a balanced evaluation of alternatives, including a realistic assessment of physical conditions.

Is delayed childbearing changing gene frequencies in Western populations?

Experimental data and clinical observations suggest that delaying childbearing influences the biology of the mother-fetus relationship, with a negative effect on fetal development and predisposition to severe diseases such as type 1 diabetes. We reason that advanced maternal age may influence intrauterine selection, favoring genotypes that are more adapted to the intrauterine environment of less young women. In the present study we have investigated the relationship of maternal age to HP genotype and PGM1-Rh area (chromosome 1) that have been previously found to be associated with fertility and developmental parameters. HP phenotype was determined in 679 consecutive puerperae from the population of central Italy. PGM1 phenotype and Rh C phenotype were determined in 222 puerperae and 200 newborns. The HP 1,1 phenotype decreases and the HP 2,2 phenotype increases with maternal age. The proportion of phenotypes carrying both the Rh C and PGM1*1 alleles is much higher in puerperae older than 36 years than in puerperae of age 22 years. The frequency of the PGM1*1-Rh C haplotype increases and the frequency of the PGM1*2-Rh C haplotype decreases with maternal age. The changes in these genetic systems with advancing maternal age are similar in mothers and newborns. The delay of childbearing age, associated in Western countries with the fertility transition in addition to detrimental effects on intrauterine development and increased susceptibility to severe disorders, could bring about changes in the genetic composition of a population.     

Ecological processes in alpine ecosystems under changing environment北大核心CSCD

[No abstract available]     

Predator–prey interactions and changing environments: who benefits?

While aquatic environments have long been thought to be more moderate environments than their terrestrial cousins, environmental data demonstrate that for some systems this is not so. Numerous important environmental parameters can fluctuate dramatically, notably dissolved oxygen, turbidity and temperature. The roles of dissolved oxygen and turbidity on predator-prey interactions have been discussed in detail elsewhere within this issue and will be considered only briefly here. Here, we will focus primarily on the role of temperature and its potential impact upon predator-prey interactions. Two key properties are of particular note. For temperate aquatic ecosystems, all piscine and invertebrate piscivores and their prey are ectothermic. They will therefore be subject to energetic demands that are significantly affected by environmental temperature. Furthermore, the physical properties of water, particularly its high thermal conductivity, mean that thermal microenvironments will not exist so that fine-scale habitat movements will not be an option for dealing with changing water temperature in lentic environments. Unfortunately, there has been little experimental analysis of the role of temperature on such predator-prey interactions, so we will instead focus on theoretical work, indicating that potential implications associated with thermal change are unlikely to be straightforward and may present a greater threat to predators than to their prey. Specifically, we demonstrate that changes in the thermal environment can result in a net benefit to cold-adapted species through the mechanism of predator-prey interactions.     

Decimal growth stages for precision wheat production in changing environments?

The utility of the decimal growth stage (DGS) scoring system for cereals is reviewed. The DGS is the most widely used scale in academic and commercial applications because of its comprehensive coverage of cereal developmental stages, the ease of use and definition provided and adoption by official agencies. The DGS has demonstrable and established value in helping to optimise the timing of agronomic inputs, particularly with regard to plant growth regulators, herbicides, fungicides and soluble nitrogen fertilisers. In addition, the DGS is used to help parameterise crop models, and also in understanding the response and adaptation of crops to the environment. The value of the DGS for increasing precision relies on it indicating, to some degree, the various stages in the development of the stem apex and spike. Coincidence of specific growth stage scores with the transition of the apical meristem from a vegetative to a reproductive state, and also with the period of meiosis, is unreliable. Nonetheless, in pot experiments it is shown that the broad period of booting (DGS 41–49) appears adequate for covering the duration when the vulnerability of meiosis to drought and heat stress is exposed. Similarly, the duration of anthesis (61–69) is particularly susceptible to abiotic stresses: initially from a fertility perspective, but increasingly from a mean grain weight perspective as flowering progresses to DGS 69 and then milk development. These associations with DGS can have value at the crop level of organisation: for interpreting environmental effects, and in crop modelling. However, genetic, biochemical and physiological analysis to develop greater understanding of stress acclimation during the vegetative state, and tolerance at meiosis, does require more precision than DGS can provide. Similarly, individual floret analysis is needed to further understand the genetic basis of stress tolerance during anthesis.     

DNA Repair: A changing geography? (1964–2008)

This article aims to explain the current state of DNA Repair studies’ global geography by focusing on the genesis of the community. Bibliometric data is used to localize scientific activities related to DNA Repair at the city level. The keyword “DNA Repair” was introduced first by American scientists. It started to spread after 1964 that is to say, after P. Howard-Flanders (Yale University), P. Hanawalt (Stanford University) and R. Setlow (Oak Ridge Laboratories) found evidence for Excision Repair mechanisms. It was the first stage in the emergence of an autonomous scientific community. In this article, we will try to assess to what extent the geo-history of this scientific field is determinant in understanding its current geography. In order to do so, we will localize the places where the first “DNA Repair” publications were signed fifty years ago and the following spatial diffusion process, which led to the current geography of the field. Then, we will focus on the evolution of the research activity of “early entrants” in relation to the activity of “latecomers”. This article is an opportunity to share with DNA Repair scientists some research results of a dynamic field in Science studies: spatial scientometrics.     

The changing bird phenology of Mid Deeside,Scotland 1974–2010

Capsule Marked changes were observed in the spring phenology of birds and were more apparent in residents and short‐distance migrants than in trans‐Mediterranean migrants.

Aims To examine changes in first songs and arrivals of birds in northeast Scotland.

Methods First song or first observations of 38 species were recorded between 1974 and 2010. Trends through time, and relationships with regional variation in temperature, were both examined.

Results There was a strong tendency for first song/first arrival dates to advance, with the average change being an advance of 25 days over the 37 years of study (or 0.7 days per year). Change was greater in the dates of first song of resident species than in the first detection of short‐distance and trans‐Mediterranean migrants. Relationships with temperature were apparent, but were significant for fewer than half of the species.

Conclusion Bird species vary greatly in their phenological response to climate warming. The recent decade of sustained higher spring temperatures has enabled greater detection of change in long‐term time series, and milder winters (except 2009/10) have also increased the incidence of wintering in short‐distance migrants.     

Will knowledge of human genome variation result in changing cancer paradigms?

Our incomplete understanding of carcinogenesis may be a significant reason why some cancer mortality rates are still increasing. This lack of understanding is likely due to a research approach that relies heavily on genetic comparison between cancerous and non-cancerous tissues and cells, which has led to the identification of genes of cancer proliferation rather than differentiation. Recent observations showing that a tremendous degree of natural human genetic variation occurs are likely to lead to a shift in the basic paradigms of cancer genetics, in that there is a need to consider both the nature of the genes involved, and the idea that not every genetic variation identified in these genes may be associated with carcinogenesis. Based on studies using LCM and micro-genetic analyses, we propose that significant cancer initiating events may take place during the very early stages of development of cancer-susceptible tissues and that using such techniques might greatly help us in our understanding of carcinogenesis.     

60Ma of legume nodulation. What's new? What's changing?

Current evidence suggests that legumes evolved about 60 million years ago. Genetic material for nodulation was recruited from existing DNA, often following gene duplication. The initial process of infection probably did not involve either root hairs or infection threads. From this initial event, two branched pathways of nodule developmental processes evolved, one involving and one not involving the development of infection threads to 'escort' bacteria to young nodule cells. Extant legumes have a wide range of nodule structures and at least 25% of them do not have infection threads. The latter have uniform infected tissue whereas those that have infection threads have infected cells interspersed with uninfected (interstitial) cells. Each type of nodule may develop indeterminately, with an apical meristem, or show determinate growth. These nodule structures are host determined and are largely congruent with taxonomic position. In addition to variation on the plant side, the last 10 years have seen the recognition of many new types of 'rhizobia', bacteria that can induce nodulation and fix nitrogen. It is not yet possible to fit these into the emerging pattern of nodule evolution.     

The changing nature of plant–microbe interactions during a biological invasion

Invasive plant species can alter belowground microbial communities. Simultaneously, the composition of soil microbial communities and the abundance of key microbes can influence invasive plant success. Such reciprocal effects may cause plant–microbe interactions to change rapidly during the course of biological invasions in ways that either inhibit or promote invasive species growth. Here we use a space-for-time substitution to illustrate how effects of soil microbial communities on the exotic legume Vicia villosa vary across uninvaded sites, recently invaded sites, and sites invaded by V. villosa for over a decade. We find that soil microorganisms from invaded areas increase V. villosa growth compared to sterilized soil or live soils collected from uninvaded sites, likely because mutualistic nitrogen-fixing rhizobia are not abundant in uninvaded areas. Notably, the benefits resulting from inoculation with live soils were higher for soils from recently invaded sites compared to older invasions, potentially indicating that over longer time scales, soil microbial communities change in ways that may reduce the success of exotic species. These findings suggest that short-term changes to soil microbial communities following invasion may facilitate exotic legume growth likely because of increases in the abundance of mutualistic rhizobia, but also indicate that longer term changes to soil microbial communities may reduce the growth benefits belowground microbial communities provide to exotic species. Our results highlight the changing nature of plant–microbe interactions during biological invasions and illustrate how altered biotic interactions could contribute to both the initial success and subsequent naturalization of invasive legume species.     

X-linked mental retardation with Marfanoid habitus: a changing phenotype with age?

In this report, we present two further examples of X-linked mental retardation with Marfanoid habitus. Follow-up data on these two patients reveal that the clinical diagnosis of this syndrome is extremely difficult, if not impossible before puberty, as the Marfanoid habitus only becomes strikingly evident during adolescence.     

Forest biodiversity in a changing climate: which logic for conservation strategies?

Climate change has direct and indirect impacts on forest ecosystems worldwide. In this context, changing site conditions and altered disturbance regimes as well as forest management responses are challenging the conservation of biodiversity in forests. Climate-induced dynamics and uncertainties related to future forest ecosystem development are calling into question current conservation strategies and concepts. Given the longevity of trees, slow development rates of forest ecosystems and slow migration rates of many forest species, the planning of adaptation measures in response to climate change are especially difficult though highly important for forest biodiversity conservation. This paper introduces a special issue with eight contributions which deal with a variety of aspects of forest biodiversity conservation in the face of climate change. More specifically, the papers address direct impacts of climate change on forest biodiversity, adaptation measures for forest and conservation management, as well as resulting challenges for conservation strategies and concepts. In conclusion, adaptation measures that enhance diversity and provide different options for future action, thereby maintaining ecosystems’ resilience, as well as conservation management operating on a landscape level, are promoted as being beneficial for coping with uncertainties related to climate change. Adaptive management, which constantly reviews conservation goals and measures, and which takes into account both science-based and local ecological knowledge on climate change can be a valuable tool to inform decisions for forest biodiversity conservation.