Is DNA barcoding child's play? Science education and the utility of DNA barcoding for the discrimination of UK tree species

We present the findings of a DNA barcoding study of the UK tree flora, implemented as part of an innovative, research‐based science education programme called ‘Tree School’. The UK tree flora comprises native and introduced species, and is a taxonomically diverse study group for the exploration of the potential and limitations of DNA barcoding. The children participating in the project collected voucher specimens and generated DNA barcode sequences from trees and shrubs found in the grounds and surrounding woodlands of a residential field centre in Dorset, UK. We assessed the potential of rbcL and matK markers for amplification and DNA sequencing success and for species discrimination among the 67 tree and shrub species included in this study. Although we achieved 100% PCR amplification and sequencing success for rbcL and matK, mononucleotide repeats affected sequence quality in matK for some taxonomic groups (e.g. Rosaceae). Species discrimination success ranged from 65% to 71% using tree‐based methods to 86% using BLASTN. The occurrence of known hybrids (diploid and polyploid) and their progenitors on the study site reduced the overall species discrimination success for both loci. This study demonstrates that, even in a floristic context, rbcL and matK alone are insufficient for the discrimination of UK tree species, especially where taxonomically complex groups are present. From a science education perspective, DNA barcoding represents a compelling and accessible platform for the engagement of non‐experts in ongoing research, providing an opportunity for them to contribute authentic scientific data to an international research campaign.     

Capture of Alouatta guariba clamitans for the surveillance of sylvatic yellow fever and zoonotic malaria: Which is the best strategy in the tropical Atlantic Forest?

Howler monkey capture is an arduous and expensive task requiring trained and specialized professionals. We compared strategies and methods to most efficiently capture Alouatta guariba clamitans in remnants of the Atlantic Forest in Rio de Janeiro and its bordering states of Minas Gerais and São Paulo. We tested whether or not the success of expeditions in the forest with anesthetic darts, nets, and baited traps differed with and without the support of an information network, a contact chain built with key institutions and inhabitants to continuously monitor howler monkey presence. The influence of forest conditions (vegetation type and fragment size) upon darting success was also evaluated. We captured 24 free‐living A. guariba clamitans. No howler monkey was caught with traps, probably due to the predominantly folivore feeding to high local plant diversity providing a great variety of food options. Captures based on an information network were significantly more efficient in terms of numbers of caught monkeys than without it. Captures with darts were considerably more efficient when performed in semideciduous forests and small forest fragments as opposed to ombrophilous forests or large woods. Although we walked great distances within the forest searching for howler monkeys, all but one animal were captured at the forest fringes. Hindrances to search and the darting method in the Atlantic Forest, for example, the steep terrain, high tree canopies, hunt pressure, and low A. guariba clamitans population density, were mitigated with the use of the information network in this monkey capture. Moreover, the information network enhanced the surveillance of zoonotic diseases, which howler monkeys and other nonhuman primates are reservoirs in Brazil, such as malaria and yellow fever.     

Evolution of wing shape in hornets: why is the wing venation efficient for species identification?

Wing venation has long been used for insect identification. Lately, the characterization of venation shape using geometric morphometrics has further improved the potential of using the wing for insect identification. However, external factors inducing variation in wing shape could obscure specific differences, preventing accurate discrimination of species in heterogeneous samples. Here, we show that interspecific difference is the main source of wing shape variation within social wasps. We found that a naive clustering of wing shape data from taxonomically and geographically heterogeneous samples of workers returned groups congruent with species. We also confirmed that individuals can be reliably attributed to their genus, species and populations on the basis of their wing shape. Our results suggested that the shape variation reflects the evolutionary history with a potential influence of other factors such as body shape, climate and mimicry selective pressures. However, the high dimensionality of wing shape variation may have prevented absolute convergences between the different species. Wing venation shape is thus a taxonomically relevant marker combining the accuracy of quantitative characters with the specificity required for identification criteria. This marker may also highlight adaptive processes that could help understand the wing's influence on insect flight.     

What is the best control strategy for multiple infectious disease outbreaks?

Effective control of infectious disease outbreaks is an important public health goal. In a number of recent studies, it has been shown how different intervention measures like travel restrictions, school closures, treatment and prophylaxis might allow us to control outbreaks of diseases, such as SARS, pandemic influenza and others. In these studies, control of a single outbreak is considered. It is, however, not clear how one should handle a situation where multiple outbreaks are likely to occur. Here, we identify the best control strategy for such a situation. We further discuss ways in which such a strategy can be implemented to achieve additional public health objectives.     

What is the best approach to treating schizophrenia in developing countries?

BACKGROUND TO THE DEBATE: Schizophrenia affects an estimated 25 million people in low- and middle-income countries, with an average lifetime risk of about 1%. The illness is associated with excess mortality from a variety of causes. A 2001 Institute of Medicine report on mental illness in developing countries found that in 1990, over two-thirds of people with schizophrenia in these countries were not receiving any treatment (http://www.nap.edu/catalog/10111.html). The report found no evidence that the proportion of treated people in the developing world had increased since 1990. There is now a debate among mental health professionals in low-income countries over how best to improve patient care. In this article, three psychiatrists give their different viewpoints on the current status of treatment efforts for schizophrenia in the developing world and the measures that can be taken to increase the proportion of patients receiving treatment.     

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states are by examining the original programs. In this study, we aim to address this issue and evaluate the reference states by a unified database and programming environment. We constructed distance-specific atomic potentials using six widely-used reference states based on 1022 high-resolution protein structures, which are applied to rank modeling in six sets of structure decoys. The reference state on random-walk chain outperforms others in three decoy sets while those using ideal-gas, quasi-chemical approximation and averaging sample stand out in one set separately. Nevertheless, the performance of the potentials relies on the origin of decoy generations and no reference state can clearly outperform others in all decoy sets. Further analysis reveals that the statistical potentials have a contradiction between the universality and pertinence, and optimal reference states should be extracted based on specific application environments and decoy spaces.     

What is natural? The scale of cryptogenesis in the North Atlantic Ocean

Aim Cryptogenic species may include those taxa that were historically introduced and are now falsely viewed as native. Investigated here is the scale of cryptogenesis in the North Atlantic Ocean by examining disjunct distributions, defined as temperate species occurring only on both sides of the North Atlantic. Disjunct distributions can be explained by four scenarios: glacial relicts, taxonomic artefacts, natural trans‐oceanic dispersal and human‐mediated introduction. Location North Atlantic Ocean. Methods Model taxa included ascidians, bivalves and hydrozoans. Biogeographic status (native, introduced or cryptogenic) was assigned to all species exhibiting a disjunct distribution, based upon multiple criteria. Results Of 1030 species, 60 have a strictly disjunct distribution. Of these disjunct species, for five species there is no reason to doubt their native status, and 55 species are cryptogenic or introduced. Groups with high relative dispersal capacities do not have disjunct distributions more often. Infaunal bivalves have the lowest relative number of disjunct species; none are cryptogenic or naturally disjunct. This supports the concept that glaciations are unlikely to cause disjunct distributions: there are no studies that provide conclusive evidence for the glacial relict model. Hydrozoa have the highest relative number of disjunct species, which, while historically explained by undocumented rafting, may more likely be the result of dispersal by ships, which travel relatively fast, are independent of currents and provide greater surface area. Main conclusions This reanalysis of the historical biogeography of the North Atlantic marine biota reveals that far more species may have been introduced than previously recognized, potentially significantly altering our fundamental understanding of community evolution and ecology. Species that have been present for centuries and can be important ecological engineers who have shaped contemporary communities are possibly falsely viewed as native: they may in fact be the unrecognized introductions of historical times.     

Ghrelin in plants: what is the function of an appetite hormone in plants?

In the present work, we provide compelling evidence for the expression of a ghrelin-like peptide hormone that has only been associated with animals, in various plant tissues. Ghrelin, the appetite stimulating hormone, has been identified from a number of different species including humans, rat, pig, mouse, gerbil, eel, goldfish, bullfrog and chicken. The study here was conducted using an immunohistochemistry assay to screen whether plants have any ghrelin immunoreactivity. In this respect, Prunus x domestica L. and Marus alba were examined. Immunohistochemistry results showed that there is a strong human ghrelin immunoreactivity substance in the parenchyma cells of these plants. This was entirely unexpected since this hormone was considered to be present solely in animals. Thus, this study is the first to report the presence of a peptide with ghrelin-like activity in plants, a finding that has only been observed in the animal kingdom. RIA analysis confirmed that these plants contain significant amounts of this substance. Furthermore, reverse-phase HPLC analyses of plant extracts showed an elution characteristic of the peptide identical to that of human ghrelin. In general, fruit from both plants had higher levels of the peptide than the vegetative parts.     

Antarctic DNA barcoding; a drop in the ocean?

Coordinated, circum-Antarctic sampling expeditions during International Polar Year 2008/09 have given access to comprehensive collections suitable for DNA barcoding. Collaborations between the Census of Antarctic Marine Life (CAML), the Marine Barcode of Life project and the Canadian Centre for DNA Barcoding have enabled the Antarctic scientific community to initiate large-scale DNA barcoding projects to record the genetic diversity of Antarctic marine fauna, coordinated by the CAML Barcoding Campaign. A total of 20,355 marine specimens from more than 2,000 morphospecies covering 18 phyla are in the processing pipeline, and to date, 11,530 sequences have been processed with the remainder due by the end of 2010. Here, we present results on the current geographic and taxonomic coverage of DNA barcode data in the Southern Ocean and identify the remaining gaps. We show how DNA barcoding in the Antarctic is answering important questions regarding marine genetic diversity and challenging current assumptions of species distribution at the poles.     

What is going on with the hormonal control of flowering in plants?

Molecular genetic studies using Arabidopsis thaliana as a model system have overwhelmingly revealed many important molecular mechanisms underlying the control of various biological events, including floral induction in plants. The major genetic pathways of flowering have been characterized in-depth, and include the photoperiod, vernalization, autonomous and gibberellin pathways. In recent years, novel flowering pathways are increasingly being identified. These include age, thermosensory, sugar, stress and hormonal signals to control floral transition. Among them, hormonal control of flowering except the gibberellin pathway is not formally considered a major flowering pathway per se, due to relatively weak and often pleiotropic genetic effects, complex phenotypic variations, including some controversial ones. However, a number of recent studies have suggested that various stress signals may be mediated by hormonal regulation of flowering. In view of molecular diversity in plant kingdoms, this review begins with an assessment of photoperiodic flowering, not in A. thaliana, but in rice (Oryza sativa); rice is a staple crop for human consumption worldwide, and is a model system of short-day plants, cereals and breeding crops. The rice flowering pathway is then compared with that of A. thaliana. This review then aims to update our knowledge on hormonal control of flowering, and integrate it into the entire flowering gene network.     

Clonal plants—What is their role in succession?

Fifteen successional seres from man-made habitats in central Europe were compared and the occurrence of clonal species assessed on the basis of cover data. The effects of soil moisture and nitrogen (expressed using Ellenberg indicator values) on the performance of clonal plants were also considered. Clonal species formed the dominant component of vegetation cover in the majority of the seres studied. In moist sites, their dominance was more pronounced and the peak in their relative cover occurred earlier in succession. The relative importance of species with guerilla type growth tended to increase with time in most seres and after 10 years these were mostly more important than those exhibiting phalanx type growth. The prevalence of guerilla species after 10 years was more obvious in moist seres. Clonal species were able to become dominant regardless of soil conditions, whereas the dominance of non-clonal species tended to be restricted to very wet and nutrient-poor sites. Clonal plant species appeared to maintain their dominance for a longer period than non-clonal plants.     

What are the genuine action potentials in plants?

This is a comment on the paper by Pyatygin in this issue [Biophysics 53(1), 81–86 (2008)], indicating some points that should be clarified to comprehensively assess the apparent diversity of plant electrical signaling.     

Native or nonnative host plants: What is better for a specialist moth?

The enemy release hypothesis (ERH) predicts that the lack of natural enemies, such as herbivores, contributes to the success of nonnative plants as colonizers. Larvae of the Neotropical specialist moth Utetheisa ornatrix (Erebidae: Arctiinae) can feed on unripe seeds and leaves of both native and nonnative Crotalaria species (Fabaceae). Despite some species being able to eat nonnative plants, such behavior can impair the herbivore, as they are not adapted to the alien plant, and still contribute to the success of the nonnative species via enemy release. We tested the performance of the moth from hatching to adulthood fed on two native (C. micans and C. paulina) and two nonnative (C. pallida, C. juncea) host plants. Utetheisa ornatrix performed better (lower development time, heavier pupae and more eggs) on the native host plants than in the nonnative. However, larva performance in nonnative C. pallida was similar to that in the native host plants. Using the larval weight 7 days after hatching from the eggs as a proxy for performance in twelve Crotalaria species (five Neotropical natives, four nonnatives from Afrotropical region, and three nonnatives from India), we found similar results. Crotalaria nutritional compounds, the defensive pyrrolizidine alkaloids and Crotalaria phylogeny did not explain moth performance. Our results give some support to the ERH. The good moth performance in nonnative C. pallida may be related to its high availability as host plant for U. ornatrix, and its longer time since their introduction in Neotropics which would provide opportunity for the moth to adapt.     

In-depth review: is hepcidin a marker for the heart and the kidney?

Iron is an essential trace element involved in oxidation–reduction reactions, oxygen transport and storage, and energy metabolism. Iron in excess can be toxic for cells, since iron produces reactive oxygen species and is important for survival of pathogenic microbes. There is a fine-tuning in the regulation of serum iron levels, determined by intestinal absorption, macrophage iron recycling, and mobilization of hepatocyte stores versus iron utilization, primarily by erythroid cells in the bone marrow. Hepcidin is the major regulatory hormone of systemic iron homeostasis and is upregulated during inflammation. Hepcidin metabolism is altered in chronic kidney disease. Ferroportin is an iron export protein and mediates iron release into the circulation from duodenal enterocytes, splenic reticuloendothelial macrophages, and hepatocytes. Systemic iron homeostasis is controlled by the hepcidin–ferroportin axis at the sites of iron entry into the circulation. Hepcidin binds to ferroportin, induces its internalization and intracellular degradation, and thus inhibits iron absorption from enterocytes, and iron release from macrophages and hepatocytes. Recent data suggest that hepcidin, by slowing or preventing the mobilization of iron from macrophages, may promote atherosclerosis and may be associated with increased cardiovascular disease risk. This article reviews the current data regarding the molecular and cellular pathways of systemic and autocrine hepcidin production and seeks the answer to the question whether changes in hepcidin translate into clinical outcomes of all-cause and cardiovascular mortality, and cardiovascular and renal end-points.

     

Oxidative Stress in Phenylketonuria: What is the Evidence?

Phenylketonuria (PKU) is an inborn error of amino acid metabolism caused by severe deficiency of phenylalanine hydroxylase activity, leading to the accumulation of phenylalanine and its metabolites in blood and tissues of affected patients. Phenylketonuric patients present as the major clinical feature mental retardation, whose pathomechanisms are poorly understood. In recent years, mounting evidence has emerged indicating that oxidative stress is possibly involved in the pathology of PKU. This article addresses some of the recent developments obtained from animal studies and from phenylketonuric patients indicating that oxidative stress may represent an important element in the pathophysiology of PKU. Several studies have shown that enzymatic and non-enzymatic antioxidant defenses are decreased in plasma and erythrocytes of PKU patients, which may be due to an increased free radical generation or secondary to the deprivation of micronutrients which are essential for these defenses. Indeed, markers of lipid, protein, and DNA oxidative damage have been reported in PKU patients, implying that reactive species production is increased in this disorder. A considerable set of data from in vitro and in vivo animal studies have shown that phenylalanine and/or its metabolites elicit reactive species in brain rodent. These findings point to a disruption of pro-oxidant/antioxidant balance in PKU. Considering that the brain is particularly vulnerable to oxidative attack, it is presumed that the administration of appropriate antioxidants as adjuvant agents, in addition to the usual treatment based on restricted diets or supplementation of tetrahydrobiopterin, may represent another step in the prevention of the neurological damage in PKU.