Using molecular tools to differentiate closely related blackfly species of the genus Simulium
J. C. Day
- Biodiversity data are the foundation for conservation and managemet and taxonomy provides the reference system, skills and tools used to identify organisms. Species level data such as species richness, composition and diversity are common metrics. However, species level identification of organisms tends to be neglected within ecological work, especially within monitoring programmes, but also in conservation biology (Giangrande, 2003). This is because collection of species level data is time consuming, with identification of species-specific characteristics traditionally involving lengthy examination of samples using microscopy. In addition it is costly and species level data is almost impossible to collect if the taxa involved are species rich and difficult to identify (Báldi 1999). Other reasons why species level identification is neglected include the fact that sample collection can damage organisms, so diagnostic morphological features are lost, or that individuals may be in a life history stage or of a sex that does not have diagnostic morphological characteristics. Furthermore, the numbers of available expert taxonomists needed for species identification are in decline and have been for several decades. Species identification using molecular taxonomy where DNA is used as a marker is championed as a tool for resolving a range of morphological problems, such as the association of all life history stages, correlating male and female specimens to the same species and identifying partial specimens. Traditional taxonomy is built around morphological variations between species, with systematic inferences based upon shared physical characters. In molecular taxonomy on the other hand, proteins and genes are used to determine evolutionary relationships. ’DNA barcoding’ aims to provide an efficient method for species-level identification and it is thought that it will provide a powerful tool for taxonomic and biodiversity research (Hajibabaei et al. 2007). Cited strengths of a molecular based approach to species identification include the potential universality and objective nature of DNA data as taxonomic information, the usefulness of molecular data in animal groups characterized by morphological cryptic characters and the use of DNA sequence information to determine otherwise ‘unidentifiable’ biological material (such as incomplete specimens or immature specimens). Its aim is to increase the speed, precision and efficiency of field studies involving diverse and difficult to identify taxa and it has the potential to be automated to provide a rapid and consistently accurate supplementary identification system to traditional taxonomy. This project was a proof-of-concept study that investigated the feasibility of using DNA barcodes to differentiate closely related blackfly species of the genus Simulium. The longer term objective would be to apply such molecular approaches to organisms used in water quality monitoring and to biodiversity studies to provide a quick, robust but practical and cost effective tool for species identification. Great Britain is currently home to 33 morphospecies of blackfly many of which are morphologically close to other species and have been the cause of much systematic revision. In addition to evaluating the use of DNA barcodes in species identification, a non-destructive DNA extraction method was developed to preserve voucher pecimens that will allow a complete morphological classification to be carried after DNA extraction. Using molecular tools to differentiate closely related blackfly species of the genus Simulium v Finding an effective DNA barcode for an individual species involves accurate taxonomic identification and the retention of voucher specimens for future morphological studies. A rapid non-destructive method for DNA extraction from small insects was developed where no clean-up step was required prior to amplification and it was possible to extract DNA of sufficient quality in minutes retaining diagnostic morphological characteristics. For any molecular tool used for species discrimination, an important consideration is defining the specific genetic loci (e.g. the position of genes on a chromosome) to be monitored. All blackfly species in this study were successfully amplified with the standard barcoding coxI gene primer pair LCO1490 5'-GGT CAA CAA ATC ATA AAG ATA TTG G-3' and HCO2198 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3' (Folmer et al. 1994) and we did not need to optimise or redesign the primer sequence.
A guide to nestling development and aging in altricial passerines
Stephanie L. Jones
Geoffrey R. Geupel
Paula J. Gouse
- Nestling growth and development studies have been a topic of interest for a greater part of the last century (Sutton 1935, Walkinshaw 1948) and continue to be of interest today. This is not surprising since studies on nestling growth can provide a wealth of biological information that has larger implications for avian management and conservation. Despite this history of studying nestling development, basic information is still limited or absent for many species. Many questions remain unanswered, and contradictory conclusions are often found in the literature (Starck and Ricklefs 1998a). Therefore, much information on aging and development can still be gained from studying the development patterns of similar species and from comparative studies, across avian orders (Minea et al. 1982, Saunders and Hansen 1989, Carsson and Hörnfeldt 1993). Additionally, nestling growth studies can yield insight into the effects of different nesting strategies on productivity (O’Connor 1978), as well as the impacts of parental effort and environmental variables on fitness (Ross 1980, Ricklefs and Peters 1981, Magrath 1991). Since low reproductive success may play a significant role in the declines of many North American passerines (Sherry and Holmes 1992, Ballard et al. 2003), a better understanding of the factors that influence reproductive success is a vital component of avian conservation (Martin 1992). Data on nestling aging can be used to improve nest survival estimates (Dinsmore 2002, Nur et al. 2004), providing information that can be used to more precisely age nests (Pinkowski 1975, Podlesack and Blem 2002), (Jones and Geupel 2007). Indeed, the relatively short time period young spend developing in the nest is a critical part of a bird’s life cycle and a nestling’s developmental path can affect its survival to independence, its survival as an adult, and its future reproductive success.
UK Seabirds in 2005 : results from the UK Seabird Monitoring Programme
- Seabirds in the UK were generally more productive in 2005 than in 2004, when productivity for many species reached an all-time low. A presumed scarcity of sandeels in 2004, especially in the North Sea, led to widespread starvation of chicks in the Northern Isles and in many places along the east coast of Britain (there is also recent evidence that prey fish were of unusually low energy content in 2004 around SE Scotland). The likely knock-on effect for 2005 was that there were few larger sandeels present (those that hatched in 2004) and it is thought that feeding on these fish allow adults to attain breeding condition in spring. This food scarcity and a cold spring led to what was among the latest breeding seasons on record. However, a late appearance of young sandeels allowed some chicks to fledge, and alternative prey species (such as sprat and small haddock) were taken also. However, it is thought that some chicks starved in this late season, as sandeels become unavailable in late summer, when they settle on the seabed. Unusually, 2005 was a very poor breeding season for many species in NW Scotland, which was spared the food shortages of 2004 and previous years; preferred prey during chick rearing were scarce in this region in 2005.
Chemical and ecological health of white sucker (Catostomus commersoni) in Rock Creek Park, Washington, D.C., 2003-04 / by Cherie V. Miller ... [et al.] ; prepared in copoeration with the National Park Service
Cherie V. Miller
Holly S. Weyers
Vicki S. Blazer
Mary E. Freeman
- Several classes of chemicals that are known or suspected contaminants were found in bed sediment in Rock Creek, including polyaromatic hydrocarbons (PAHs), phthalate esters, organochlorine pesticides, dioxins and furans, trace metals and metalloids (mercury, arsenic, cadmium, chromium, cobalt, copper, lead, nickel, silver, and zinc), and polychlorinated biphenyls (total PCBs and selected aroclors). Concentrations of many of these chemicals consistently exceeded thresholdor chronic-effects guidelines for the protection of aquatic life and often exceeded probable effects levels (PELs). Exceedance of PELs was dependent on the amount of total organic carbon in the sediments. Concurrent with the collection of sediment-quality data, white sucker (Catostomus commersoni) were evaluated for gross-external and internal-organ anomalies, whole-body burdens of chemical contaminants, and gut contents to determine prey. The histopathology of internal tissues of white sucker was compared to contaminant levels in fish tissue and bed sediment. Gut contents were examined to determine preferential prey and thus potential pathways for the bioaccumulation of chemicals from bed sediments. Male and female fish were tested separately. Lesions and other necroses were observed in all fish collected during both years of sample collection, indicating that fish in Rock Creek have experienced some form of environmental stress. No direct cause and effect was determined for chemical exposure and compromised fish health, but a substantial weight of evidence indicates that white sucker, which are bottom-eeding fish and low-order consumers in Rock Creek, are experiencing some reduction in vitality, possibly due to immunosuppression. Abnormalities observed in gonads of both sexes of white sucker and observations of abnormal behavior during spawning indicated some interruption in reproductive success.
Performance and storage requirements of topology-conserving maps for robot manipulator control
Rüdiger W. Brause
- A new programming paradigm for the control of a robot manipulator by learning the mapping between the Cartesian space and the joint space (inverse Kinematic) is discussed. It is based on a Neural Network model of optimal mapping between two high-dimensional spaces by Kohonen. This paper describes the approach and presents the optimal mapping, based on the principle of maximal information gain. It is shown that Kohonens mapping in the 2-dimensional case is optimal in this sense. Furthermore, the principal control error made by the learned mapping is evaluated for the example of the commonly used PUMA robot, the trade-off between storage resources and positional error is discussed and an optimal position encoding resolution is proposed.
Comment on the European Parliament Draft Report on the proposal for a recovery and resolution directive : (Rapporteur: Gunnar Hökmark)
– Doc 2012/0150 (COD) of 11 October 2012 –
Jan Pieter Krahnen
- This present comment suggests an amendment to the proposal for a directive of the European Parliament and of the Council, establishing a framework for the recovery and resolution of credit institutions and investment firms. The current proposal focuses on bail-in, but does not sufficiently take into account the pressure exerted on central bankers, supervisors and politicians by the fear of interbank contagion. The only way out of this hold-up type of situation can be found in bail-in bonds. Bail-in bonds are dedicated loss taking debt instruments, whose status of being first in line if it comes to default is clearly communicated from day one.
General cost analysis for scholarly communication in Germany : results of the "Houghton Report" for Germany
John W. Houghton
- Management Summary: Conducted within the project “Economic Implications of New Models for Information Supply for Science and Research in Germany”, the Houghton Report for Germany provides a general cost and benefit analysis for scientific communication in Germany comparing different scenarios according to their specific costs and explicitly including the German National License Program (NLP).
Basing on the scholarly lifecycle process model outlined by Björk (2007), the study compared the following scenarios according to their accounted costs:
- Traditional subscription publishing,
- Open access publishing (Gold Open Access; refers primarily to journal publishing where access is free of charge to readers, while the authors or funding organisations pay for publication)
- Open Access self-archiving (authors deposit their work in online open access institutional or subject-based repositories, making it freely available to anyone with Internet access; further divided into (i) CGreen Open Access’ self-archiving operating in parallel with subscription publishing; and (ii) the ‘overlay services’ model in which self-archiving provides the foundation for overlay services (e.g. peer review, branding and quality control services))
- the NLP.
Within all scenarios, five core activity elements (Fund research and research communication; perform research and communicate the results; publish scientific and scholarly works; facilitate dissemination, retrieval and preservation; study publications and apply the knowledge) were modeled and priced with all their including activities.
Modelling the impacts of an increase in accessibility and efficiency resulting from more open access on returns to R&D over a 20 year period and then comparing costs and benefits, we find that the benefits of open access publishing models are likely to substantially outweigh the costs and, while smaller, the benefits of the German NLP also exceed the costs.
This analysis of the potential benefits of more open access to research findings suggests that different publishing models can make a material difference to the benefits realised, as well as the costs faced. It seems likely that more Open Access would have substantial net benefits in the longer term and, while net benefits may be lower during a transitional period, they are likely to be positive for both ‘author-pays’ Open Access publishing and the ‘over-lay journals’ alternatives (‘Gold Open Access’), and for parallel subscription publishing and self-archiving (‘Green Open Access’). The NLP returns substantial benefits and savings at a modest cost, returning one of the highest benefit/cost ratios available from unilateral national policies during a transitional period (second to that of ‘Green Open Access’ self-archiving). Whether ‘Green Open Access’ self-archiving in parallel with subscriptions is a sustainable model over the longer term is debateable, and what impact the NLP may have on the take up of Open Access alternatives is also an important consideration. So too is the potential for developments in Open Access or other scholarly publishing business models to significantly change the relative cost-benefit of the NLP over time.
The results are comparable to those of previous studies from the UK and Netherlands. Green Open Access in parallel with the traditional model yields the best benefits/cost ratio. Beside its benefits/cost ratio, the meaningfulness of the NLP is given by its enforceability. The true costs of toll access publishing (beside the buyback” of information) is the prohibition of access to research and knowledge for society.
"Open forum on Germany’s banking system"
- Conference organized jointly by: Elena Carletti (Center for Financial Studies) Jörg Decressin (International Monetary Fund) Jan Pieter Krahnen (University of Frankfurt and Center for Financial Studies) Christian Ossig (Center for Financial Studies) Conference Reader Nr. 2006/01
Report: Cultural Research Centre (CRC)
- This report arises from research carried out in Iganga and Namutumba districts in late 2006/early 2007 by the Cultural Research Centre (CRC), based in Jinja. Our research focus was to gauge the impact of using Lusoga as a medium of instruction (since 2005 in "pilot" lower primary classes) within and outside the classroom. This initiative was in response to a new set of circumstances in the education sector in Uganda, especially the introduction by Government of teaching in local languages in lower primary countrywide from February 2007. This followed an experimental period, in selected pilot districts, including Iganga, where fifteen pilot schools had been chosen: all these became part of this study.
APNET - ADEA study project on intra African book trade
- Following on the ADEA/APNET study on inter-African Book trade that was commissioned in 1999, ADEA tasked APNET to facilitate the production of national book industry updates in each country. The updates are aimed at encouraging commercial development of inter-African book trade and to make available to the public, total systematic and current situations on the book trade in each country.