bluuebunny/crossref_metadata_2025_split huggingface dataset:
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
Authors: EPP LAURA S. , BOESSENKOOL SANNE , BELLEMAIN EVA P. , HAILE JAMES , ESPOSITO ALFONSO , RIAZ TIAYYBA , ERSÉUS CHRISTER , GUSAROV VLADIMIR I. , EDWARDS MARY E. , JOHNSEN ARILD , STENØIEN HANS K. , HASSEL KRISTIAN , KAUSERUD HÅVARD , YOCCOZ NIGEL G. , BRÅTHEN KARI ANNE , WILLERSLEV ESKE , TABERLET PIERRE , COISSAC ERIC , BROCHMANN CHRISTIAN 
Published: April 2012

AbstractMetabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late‐Pleistocene age (∼16 000–50 000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.
Next‐generation sequencing technologies for environmental DNA research
Authors: SHOKRALLA SHADI , SPALL JENNIFER L. , GIBSON JOEL F. , HAJIBABAEI MEHRDAD 
Published: April 2012

AbstractSince 2005, advances in next‐generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species‐specific DNA barcodes has been a key application of next‐generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next‐generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next‐generation sequencing technologies in regard to their application for environmental DNA analysis.
Bioinformatic challenges for DNA metabarcoding of plants and animals
Authors: COISSAC ERIC , RIAZ TIAYYBA , PUILLANDRE NICOLAS 
Published: April 2012

AbstractAlmost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under‐explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom‐made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.
Postglacial colonization of Europe by the barbastelle bat: agreement between molecular data and past predictive modelling
Authors: REBELO HUGO , FROUFE ELSA , BRITO JOSÉ C. , RUSSO DANILO , CISTRONE LUCA , FERRAND NUNO , JONES GARETH 
Published: April 2012

AbstractThe barbastelle (Barbastella barbastellus) is a rare forest bat with a wide distribution in Europe. Here, we combine results from the analysis of two mtDNA fragments with species distribution modelling to determine glacial refugia and postglacial colonization routes. We also investigated whether niche conservatism occurs in this species. Glacial refugia were identified in the three southern European peninsulas: Iberia, Italy and the Balkans. These latter two refugia played a major role in the postglacial colonization process, with their populations expanding to England and central Europe, respectively. Palaeo‐distribution models predicted that suitable climatic conditions existed in the inferred refugia during the last glacial maximum (LGM). Nevertheless, the overlap between the current and the LGM distributions was almost inexistent in Italy and in the Balkans, meaning that B. barbastellus populations were forced to shift range between glacial and interglacial periods, a process that probably caused some local extinctions. In contrast, Iberian populations showed a ‘refugia within refugium’ pattern, with two unconnected areas containing stable populations (populations that subsisted during both glacial and interglacial phases). Moreover, the match between LGM models and the refugial areas determined by molecular analysis supported the hypothesis of niche conservatism in B. barbastellus. We argue that geographic patterns of genetic structuring, altogether with the modelling results, indicate the existence of four management units for conservation: Morocco, Iberia, Italy and UK, and Balkans and central Europe. In addition, all countries sampled possessed unique gene pools, thus stressing the need for the conservation of local populations.
Large‐scale study of the interactions between proteins involved in type IV pilus biology in Neisseria meningitidis: characterization of a subcomplex involved in pilus assembly
Authors: Georgiadou Michaella , Castagnini Marta , Karimova Gouzel , Ladant Daniel , Pelicic Vladimir 
Published: April 2012

SummaryThe functionally versatile type IV pili (Tfp) are one of the most widespread virulence factors in bacteria. However, despite generating much research interest for decades, the molecular mechanisms underpinning the various aspects of Tfp biology remain poorly understood, mainly because of the complexity of the system. In the human pathogen Neisseria meningitidis for example, 23 proteins are dedicated to Tfp biology, 15 of which are essential for pilus biogenesis. One of the important gaps in our knowledge concerns the topology of this multiprotein machinery. Here we have used a bacterial two‐hybrid system to identify and quantify the interactions between 11 Pil proteins from N. meningitidis. We identified 20 different binary interactions, many of which are novel. This represents the most complex interaction network between Pil proteins reported to date and indicates, among other things, that PilE, PilM, PilN and PilO, which are involved in pilus assembly, indeed interact. We focused our efforts on this subset of proteins and used a battery of assays to determine the membrane topology of PilN and PilO, map the interaction domains between PilE, PilM, PilN and PilO, and show that a widely conserved N‐terminal motif in PilN is essential for both PilM–PilN interactions and pilus assembly. Finally, we show that PilP (another protein involved in pilus assembly) forms a complex with PilM, PilN and PilO. Taken together, these findings have numerous implications for understanding Tfp biology and provide a useful blueprint for future studies.
Genotyping of HPA‐1 to ‐7 and ‐15 in the Thai population using multiplex PCR
Authors: Kengkate M. , Butthep P. , Kupatawintu P. , Kanunthong S. , Chantratita W. , Nathalang O. 
Published: April 2012

Background: Different polymerase chain reaction (PCR) techniques for human platelet antigens (HPA) genotyping have been implemented, in order to diagnose the clinical syndromes of patients with thrombocytopaenia and provide effective HPA‐matched platelet donors.Objectives: The aim of this study is to develop an in‐house multiplex PCR for HPA‐1 to ‐7 and ‐15 genotyping in the Thai population.Methods: One hundred DNA samples of known HPA genotyping by the PCR with sequence‐specific primers (PCR‐SSP), as previously described, were tested with the multiplex PCR. Additionally, 300 DNA samples of group O donors were tested for HPA‐1 to ‐7 and ‐15 genotyping using multiplex PCR.Results: The comparison of HPA‐1 to ‐7 and ‐15 genotype results between multiplex PCR and PCR‐SSP technique was in 100% concordance. Interestingly, HPA‐2b2b genotype was found in two samples; however, other low‐incidence genotypes such as HPA‐1b1b, HPA‐5b5b, HPA‐6b6b and HPA‐7b7b were not found in this study. Moreover, 30 samples were randomly tested twice for HPA genotyping using the multiplex PCR and demonstrated reproducible results.Conclusions: This study shows that the in‐house multiplex PCR is simple, cost‐effective and suitable for HPA genotyping for routine laboratories in other developing countries. Nevertheless, a large‐scale evaluation of this technique through multicentre analysis is suggested.
Community participation and voice mechanisms under performance‐based financing schemes in Burundi
Authors: Falisse Jean‐Benoît , Meessen Bruno , Ndayishimiye Juvénal , Bossuyt Michel 
Published: April 2012

AbstractObjective  Community participation is often described as a key for primary health care in low‐income countries. Recent performance‐based financing (PBF) initiatives have renewed the interest in this strategy by questioning the accountability of those in charge at the health centre (HC) level. We analyse the place of two downward accountability mechanisms in a PBF scheme: health committees elected among the communities and community‐based organizations (CBOs) contracted as verifiers of health facilities’ performance.Method  We evaluated 100 health committees and 79 CBOs using original data collected in six Burundi provinces (2009–2010) and a framework based on the literature on community participation in health and New Institutional Economics.Results  Health committees appear to be rather ineffective, focusing on supporting the medical staff and not on representing the population. CBOs do convey information about the concerns of the population to the health authorities; yet, they represent only a few users and lack the ability to force changes. PBF does not automatically imply more ‘voice’ from the population, but introduces an interesting complement to health committees with CBOs. However, important efforts remain necessary to make both mechanisms work. More experiments and analysis are needed to develop truly efficient ‘downward’ mechanisms of accountability at the HC level.
Recombinant factor VIIa as last‐resort treatment of desperate haemorrhage
Authors: PALMASON R. , VIDARSSON B. , SIGVALDASON K. , INGIMARSSON J. P. , GUDBJARTSSON T. , SIGURDSSON G. H. , ONUNDARSON P. T. 
Published: April 2012

IntroductionStudies are inconclusive regarding clinical outcomes after administration of recombinant activated coagulation factor VII (rFVIIa) during severe haemorrhage. The circumstances encountered during desperate haemorrhage make it difficult to include the most critically ill patients that could possibly benefit the most from such treatment into randomized controlled trials. We report our experience with rFVIIa as last‐resort treatment of desperate haemorrhage when all standard treatment has failed.Materials and MethodsHospital charts of all consecutive patients treated with rFVIIa for desperate non‐haemophilic bleeding over a 10‐year period at the single institution administering rFVIIa were surveyed for treatment indications, clinical outcome, transfusion need and coagulation profiles.ResultsFifty‐five rFVIIa treatment occasions of desperate bleeding were identified in 54 patients (median age 54 years). A single rFVIIa dose was used in 86%, and haemorrhage was considered effectively contained by immediate clinical response on 81% of occasions. Overall, 38 patients (71%) survived for over 30 days. Two thromboembolic events occurred (3.6%). The 24‐h mortality in 45 rFVIIa immediate clinical responders and 10 non‐responders was 2% and 50%, respectively (P = 0.0004), and the 30‐day mortality was 25% and 60%, respectively (P = 0.05). Blood product use decreased with rFVIIa (P < 0.01) as did the prothrombin time (20.0‐13.3 s, P < 0.0001).ConclusionsThe majority of unselected consecutive patients receiving rFVIIa as last‐resort treatment for desperate haemorrhage were considered to have immediate clinical response as well as reduced transfusion requirements and correction of coagulation parameters. An immediate clinical response to rFVIIa may possibly be predictive of survival.
Improvement of the photosynthetic characteristics of transgenic wheat plants by transformation with the maize C4 phosphoenolpyruvate carboxylase gene
Authors: Hu Lin , Li Yan , Xu Weigang , Zhang Qingchen , Zhang Lei , Qi Xueli , Dong Haibin 
Published: April 2012

With 7 figures and 2 tablesAbstractAttempts have been made to transform C3 crops with C4 genes to improve the photosynthetic rate of C3 plants. In our study, a full‐length cDNA for phosphoenolpyruvate carboxylase gene (pepc) was isolated from Zea mays by PCR. The pepc gene was introduced into wheat plants (Triticum aestivum) by particle bombardment transformation. The integration, transcription and expression of the pepc gene were confirmed by Southern blot, RT‐PCR and Western blot analysis. Physiological studies showed that phosphoenolpyruvate carboxylase activity in the transgenic plants was 140% higher than that of the untransformed plants. The highest rate of photosynthesis in the transgenic plants was 31.95 μmol CO2/m2/s, which was 26% greater than the rate in untransformed plants. The light saturation point and carboxylation efficiency of pepc transgenic wheat were 20% and 22.57% higher, respectively, than those of untransformed wheat. As a result, the weight of seed per spike and thousand‐grain weight were 0.23 g and 1.21 g higher than those of untransformed wheat. Our research will facilitate the further study of the function of the pepc gene in wheat plants.
Improving in vivo maize doubled haploid production efficiency through early detection of false positives
Authors: Choe Eunsoo , Carbonero Christine Hayot , Mulvaney Kelly , Rayburn A. Lane , Mumm Rita H. 
Published: April 2012

With 1 figure and 2 tablesAbstractIn vivo doubled haploid (DH) technology provides a means of creating new maize inbred lines relatively quickly; however, productivity is limited by false‐positive (FP) plants for haploidy and for dihaploidy, which consume resources of space and labour until detected. This work examines the potential for using stomata guard cell length measurement as a means for early detection of FP plants. We found that the true haploid and DH plants could be differentiated from FP and untreated diploid controls as early as Leaf 2 stage by stomata guard cell length measurement. Furthermore, DH plants were distinguishable from haploid and other diploid plants by the Leaf 7 growth stage. Results suggest that, when used together with screening through the anthocyanin colour marker system and flower fertility, stomata guard cell measurement is an easy, non‐destructive, early screening method that may lead to a greater efficiency in DH production systems and optimization of resource allocation for space and labour.
Evidence of the existence of a toxic form of Cylindrospermopsis raciborskii (Nostocales, Cyanobacteria) in Japan
Authors: Zarenezhad Saghar , Sano Tomoharu , Watanabe Makoto M. , Kawachi Masanobu 
Published: April 2012

SUMMARYCylindrospermopsis raciborskii is a common, bloom‐forming, planktonic, freshwater cyanobacterium. Toxic populations producing cylindrospermopsin can cause water‐safety problems. Although C. raciborskii is distributed worldwide, the presence of cylindrospermopsin‐producing strains of C. raciborskii was initially reported only in Australia and recently in Thailand. Here, we report the isolation of a toxic strain of C. raciborskii (ISG9) from a freshwater sample collected in Okinawa in 2008. This is the first report describing toxin expression in this species in Japan, detected from a subtropical area. The C. raciborskii species is known to produce cylindrospermopsin as a dominant toxin; however, in this new isolate, the dominant toxin expressed was deoxy‐cylindrospermopsin. The discovery of a toxic strain of C. raciborskii in southern Japan emphasizes the need for basic monitoring schemes for this species in water supplies located in the temperate regions of Japan because of its possible expansion and distribution to other geographic areas.
Prospective evaluation of the optimal number of 25‐gauge needle passes for endoscopic ultrasound‐guided fine‐needle aspiration biopsy of solid pancreatic lesions in the absence of an onsite cytopathologist
Authors: Suzuki Rei , Irisawa Atsushi , Bhutani Manoop S. , Hikichi Takuto , Takagi Tadayuki , Sato Ai , Sato Masaki , Ikeda Tsunehiko , Watanabe Ko , Nakamura Jun , Tasaki Kazuhiro , Obara Katsutoshi , Ohira Hiromasa 
Published: April 2012

Introduction:  A prior study with 22‐gauge needles recommended more than seven needle passes for endoscopic ultrasound‐guided fine‐needle aspiration biopsy (EUS‐FNA) of solid pancreatic lesions (SPL) without onsite cytopathology for optimal acquisition of cytopathological diagnosis. The feasibility of this recommendation should be re‐evaluated considering the later development and popularity of 25‐gauge EUS‐FNA needles. We aimed to determine the optimal number of needle passes for cytopathological specimen acquisition with 25‐gauge needles for EUS‐FNA of SPL.Methods:  A preliminary prospective study of 22 patients with an onsite cytopathology technician showed a sensitivity of 93.3% and a specificity of 100% with four needle passes that was not statistically different from five needle passes. Based on our preliminary study, we fixed the number of needle passes to four (Group A). As a control group, we carried out sampling in consecutive patients using 25‐gauge needles with an onsite cytopathologist (Group B). Sampling rate, diagnostic value and complications were evaluated.Results:  We enrolled 20 patients in each group. Sampling rate was higher in Group B (20/20, 100%) than in Group A (19/20, 95%), but there was no statistical difference between them (P‐value = 0.31). In Group A, sensitivity, specificity and accuracy were 100% among 19. In Group B, sensitivity was 94.1%, specificity 100%, accuracy 95%. There were also no statistical differences between the groups. No complications were seen.Conclusion:  Our study suggests that four needle passes using a 25‐gauge needle may be sufficient for EUS‐FNA of SPL where onsite cytology is not available.
The value of coordinated management of interacting ecosystem services
Authors: White Crow , Costello Christopher , Kendall Bruce E. , Brown Christopher J. 
Published: April 2012

Ecology Letters (2012)AbstractCoordinating decisions and actions among interacting sectors is a critical component of ecosystem‐based management, but uncertainty about coordinated management’s effects is compromising its perceived value and use. We constructed an analytical framework for explicitly calculating how coordination affects management decisions, ecosystem state and the provision of ecosystem services in relation to ecosystem dynamics and socio‐economic objectives. The central insight is that the appropriate comparison strategy to optimal coordinated management is optimal uncoordinated management, which can be identified at the game theoretic Nash equilibrium. Using this insight we can calculate coordination’s effects in relation to uncoordinated management and other reference scenarios. To illustrate how this framework can help identify ecosystem and socio‐economic conditions under which coordination is most influential and valuable, we applied it to a heuristic case study and a simulation model for the California Current Marine Ecosystem. Results indicate that coordinated management can more than double an ecosystem’s societal value, especially when sectors can effectively manipulate resources that interact strongly. However, societal gains from coordination will need to be reconciled with observations that it also leads to strategic simplification of the ecological food web, and generates both positive and negative impacts on individual sectors and non‐target species.
Environment‐dependent selection on mate choice in a natural population of birds
Authors: Robinson Matthew R. , Sander van Doorn G. , Gustafsson Lars , Qvarnström Anna 
Published: April 2012

AbstractFemale mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals.
Does increasing mortality change the response of fish populations to environmental fluctuations?
Authors: Rouyer Tristan , Sadykov Alexander , Ohlberger Jan , Stenseth Nils Chr. 
Published: April 2012

Ecology Letters (2012) 15: 658–665AbstractFluctuations of fish populations abundances are shaped by the interplay between population dynamics and the stochastic forcing of the environment. Age‐structured populations behave as a filter of the environment. This filter is characterised by the species‐specific life cycle and life‐history traits. An increased mortality of mature individuals alters these characteristics and may therefore induce changes in the variability of populations. The response of a generic age‐structured model was analysed to investigate the expected changes in the fluctuations of fish populations in response to decreased adult survival. These expectations were then tested on an extensive dataset. In accordance with theory, the analyses revealed that decreased adult survival and mean age of spawners were linked to an increase in the relative importance of short‐term fluctuations. It suggests that intensive exploitation can lead to a change in the variability of fish populations, an issue of central interest from both conservation and management perspectives.