bluuebunny/crossref_metadata_2025_split huggingface dataset:
DETERMINATION OF DRYING PARAMETERS, ASCORBIC ACID CONTENTS AND COLOR CHARACTERISTICS OF NETTLE LEAVES DURING MICROWAVE‐, AIR‐ AND COMBINED MICROWAVE–AIR‐DRYING
Authors: ALIBAS ILKNUR 
Published: April 2009

ABSTRACT Nettle leaves (Urtica dioica L.), with a moisture of 4.41 (dry basis [d.b .]), were dried using three drying methods: microwave, air and combined microwave–air. Drying continued until leaf moisture decreased to 0.1 (d.b .). Three different microwave output powers, 160, 350 and 500 W, were used in the microwave‐drying. Drying treatments in air‐drying were 50, 75 and 100C, and 1 m/s fan speed. The combination drying, in which microwave‐ and air‐drying were applied together, was nine different combination levels. Drying periods lasted for 6–14, 40–120 and 2–12 min for microwave‐, air‐ and combined microwave–air‐drying, respectively, depending on the drying level. Energy consumption was 0.07–0.10, 0.25–0.34 and 0.08–0.16 kWh, respectively. In this study, measured values were compared with the predicted values obtained from Page's semiempirical equation. Optimum drying period, color and energy consumption were obtained when microwave‐ and air‐drying were applied simultaneously and the optimum combination level was 500‐W microwave applications at 50C.PRACTICAL APPLICATIONSMicrowave‐, air‐ and combined microwave–air‐drying have been industrially applied in the drying of foodstuffs, and pharmaceutical and biologic products. The use of a combined microwave–air dryer is common in the food industry. Applied examples include the serial or a parallel combination of bothmethods. The application of the microwave as a heat source produces a fast drying rate and higher drying quality.Tunnel‐type microwave–air dryers have been recently used in the industry, and they can be used for the drying of foods, wood and paper products, traditional medicine solid preparations, crude drugs and sliced herbal medicines. They have the virtues of rapid drying, well distributed, energy saving, high efficiency, easy to operate and control, safety and nonpollution, etc.
Quality counts: new parameters in blood cell counting
Authors: BRIGGS C. 
Published: April 2009

SummaryRecently several parameters have been introduced to the complete blood count such as nucleated red blood cells, immature granulocytes; immature reticulocyte fraction, immature platelet fraction and red cell fragments as well as new parameters for detection of functional iron deficiency. Leucocyte positional parameters, which may diagnose specific diseases (e.g. differentiate between abnormal lymphocytes in leukaemia and viral conditions and may also detect malarial infection) are now available. At this time they are only used for research; however, generally such parameters later become reportable. One manufacturer’s routine analyser allows measurement of cells by flow cytometry using monoclonal antibodies. Currently, there are no accredited external quality assessment schemes (EQAS) for these parameters. For a number of parameters, on some instruments, there is no internal quality control, which brings into question whether these parameters should be used for clinical decision making. Other more established parameters, such as mean platelet volume, red cell distribution width and the erythrocyte sedimentation rate do not have EQAS available. The UK National EQAS for General Haematology held a workshop earlier this year in 2008 to discuss these parameters. Participants were asked to provide a consensus opinion on which parameters are the most important for inclusion in future haematology EQAS.
Predicting range overlap in two closely related species of spiders
Authors: ANDERSON BARBARA J. , BAI YIXUAN , THOMAS CHRIS D. , OXFORD GEOFF S. 
Published: April 2009

Abstract.

Predicting when and where species are likely to experience inter‐specific interactions as a result of climate change may be as relevant to understanding their evolutionary futures as predicting responses to physical environmental variables.
In this paper, models built using data for the distributions of two species of large house spider, Tegenaria saeva and T. gigantea (Agelenidae), from relatively long‐established parts of their ranges are used to predict species overlap in a region of more recent range expansion.
Generalised linear models (GLMs) are used to identify the key environmental variables associated with the distributions of the spider species in an east–west band across central Britain. Using this model, the distributions of the two species both north and south of the central band are predicted and tested for how closely they matched observed distributions, and thus whether environmental factors are a sufficient explanation for current distribution patterns in England and Wales.
Results demonstrate that predictions of both species distributions and overlap in the south region are almost as good as in the model‐building zone, but that predicted distributions in the north are no better than random. Here either climate is of no importance in determining species distributions or, perhaps more likely, the system is still in a state of flux and currently reflects the stochasticity of recent colonisation.
Further long‐term monitoring of the populations may allow discrimination between alternative hypotheses that could explain the current mismatch between climate and species’ distributions.
Express barcodes: racing from specimen to identification
Authors: IVANOVA NATALIA V. , BORISENKO ALEX V. , HEBERT PAUL D. N. 
Published: April 2009

AbstractAlthough devices combining microfluidic and advanced sequencing technologies promise a future where one can generate a DNA barcode in minutes, current analytical regimes typically involve workflows that extend over 2 days. Here we describe simple protocols enabling the advance from a specimen to barcode‐based identification in less than 2 h. The protocols use frozen or lyophilized reagents that can be prepackaged into ‘kits’ and support barcode analysis across the animal kingdom. The analytical procedure allows 5 min for DNA extraction, 25 min for polymerase chain reaction amplification of the barcode region, 25 min for cycle‐sequencing, 10 min for cleanup, 45 min for capillary sequencing and 5 min for trace file analysis to complete DNA‐based identification. This study involved the comparison of varied DNA preservation and extraction methods, and evaluatedTaqpolymerases with high processivity and resistance to inhibitors.
Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia
Authors: SAUNDERS GARY W. 
Published: April 2009

AbstractAs part of an extensive DNA‐based floristic survey of marine macroalgae in Canadian waters, an unexpected sequence for a Gracilaria sp. was generated from British Columbia. Before further molecular analyses and corresponding morphological/anatomical observations this mystery sequence was temporarily entered into our database as Gracilaria BCsp. Continued sampling uncovered this species from four additional locations. A timely collaboration with international colleagues introduced sequences from the invasive Gracilaria vermiculophylla into our cytochrome c oxidase I alignments — these a perfect match to BCsp indicating that this species occurs in British Columbia. A discussion of the origin of this taxon in Canadian waters, whether natural or introduced, is provided.
DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India
Authors: RAGUPATHY SUBRAMANYAM , NEWMASTER STEVEN G. , MURUGESAN MARUTHAKKUTTI , BALASUBRAMANIAM VELUSAMY 
Published: April 2009

AbstractOur research brought together traditional aboriginal knowledge (TK) and scientific knowledge (SK) to explore the relationship between scientific and aboriginal systems of botanical classification and the corresponding valorization(s) of biological diversity in the Western Ghats of southern India. We worked with two aboriginal cultures namely ‘Irulas’ and ‘Malasars’ of the Nilgiri Biosphere Reserve with an objective of evaluating the ability of different knowledge systems (SK and TK) to distinguish grass species belonging to the genus Tripogon, and assess the ability of DNA barcoding to discriminate a new cryptic species ‘Tripogon cope’ as deciphered by the hill tribes. We discovered that the aboriginal informants identified a common ethnotaxa ‘Sunai pul’, which is a cryptic species of grass not recognized by the SK classification.'sunai pul’ is very important to both aboriginal cultures with ritualistic and economic utility. Morphometric analysis confirms the cryptic nature of this new species, which was validated using DNA barcoding. DNA barcode regions matK and trnH‐psbA showed distinct sequence variations among the closely related ethnotaxa. Given the cryptic nature of ethnotaxa, we propose that a DNA barcode may be a reliable tool to identify ethnotaxa. We have initiated further studies in other cultures to develop theoretically sophisticated insights concerning the encounter between ‘local’ and ‘scientific’ approaches to the use of biodiversity knowledge. Furthermore, the research will add to a unifying global effort to speed up the documentation and understanding of the planet's natural diversity, while simultaneously respecting the cultural heterogeneity as a vital component of biological diversity.
DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional‐scale approach
Authors: RADULOVICI ADRIANA E. , SAINTE‐MARIE BERNARD , DUFRESNE FRANCE 
Published: April 2009

AbstractMarine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78–13.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.
DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea)
Authors: FOOTTIT R. G. , MAW H. E. L. , HAVILL N. P. , AHERN R. G. , MONTGOMERY M. E. 
Published: April 2009

AbstractThe Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658‐bp barcode fragment from the 5′‐end of the mitochondrial cytochrome c oxidase 1 gene (COI) in differentiating among 17 species of Adelgidae, in associating life‐cycle stages, and in assessing patterns of geographical variation in selected species. Species of Adelgidae are well‐differentiated by DNA barcodes, enabling the identification of different morphological forms, immature stages and individuals on different hosts and at different periods of the life cycle. DNA barcodes have uncovered cryptic diversity within taxa and, in other cases, a lack of sequence divergence in species pairs previously separated by life‐cycle characteristics, indicating a need for further taxonomic analysis.
DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies
Authors: SHEFFIELD CORY S. , HEBERT PAUL D. N. , KEVAN PETER G. , PACKER LAURENCE 
Published: April 2009

AbstractDNA barcoding has been evaluated for many animal taxa and is now advocated as a reliable and rapid means for species‐level identification. The coming‐to‐light of this identification tool is timely as we are now facing perhaps the greatest rate of species loss in recent millennia. This study contributes to an ever‐increasing number of published accounts of DNA barcoding successfully and accurately distinguishing animal taxa, in this instance, the bee fauna of Nova Scotia, Canada. Most members of this well‐known fauna were resolved with particular clarity; the average intraspecific divergence was less than 0.5%, and COI sequences from over 75% of the province's species are now in the Barcodes of Life Data System. DNA barcoding also revealed some surprises within this fauna, including the possible recognition of two undescribed genetically unique species, one in the genusCeratina(subgenusZadontomerus), the second in the genusAndrena(subgenusLarandrena); both are presently receiving further taxonomic study. In addition, DNA barcoding has allowed sex‐associations among two pairs of cleptoparasitic species. The resulting utility of DNA barcoding for ecological studies of bee communities is discussed.
Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera: Coleophoridae: Momphinae:Mompha)
Authors: EMERY VIRGINIA J. , LANDRY JEAN‐FRANÇOIS , ECKERT CHRISTOPHER G. 
Published: April 2009

AbstractClose interactions between insects and plants have played a major role in the evolution of both these diverse groups of organisms. Studying these interactions, however, can be difficult because many insects, especially parasites, impinge most strongly on plants during larval stages when they are morphologically difficult to identify, and many belong to diverse groups for which most species remain undescribed. We used DNA barcoding to identify nondescript lepidopteran larvae that regularly parasitize flower buds of the coastal dune endemicCamissoniopsis cheiranthifolia(Onagraceae). We obtained cytochrome oxidase 1 mitochondrial DNA sequences from 201 parasite specimens from across the host geographical range. The Barcode of Life Database Identification System combined with Bayesian analysis grouped all 15 parasite haplotypes in a distinct, monophyletic clade within the genusMompha(Lepidoptera: Coleophoridae: Momphinae), a group known to be host specialists on plants of the Onagraceae. Species identity and phylogenetic affinities withinMomphacould not be confirmed because few barcode sequences exist from this diverse and poorly known group of moths. However, morphological analysis, including detailed dissection of genitalia for a subsample of 23 reared adults and comparison with known species ofMompha, also indicated that the larvae parasitizingC. cheiranthifoliaconstitute a distinct and undescribed species within this genus. Knowing that floral parasitism ofC. cheiranthifoliainvolves a single, putatively host‐specific microlepidopteran greatly facilitates formulating and testing hypotheses concerning how floral parasitism has promoted the evolution of striking floral diversity within this species. More generally, DNA barcoding combined with morphological analysis can greatly hasten identification of problematic specimens and enhance our understanding of the diversity, ecology and evolution of plant–insect interactions.
Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae)
Authors: RIVERA JULIO , CURRIE DOUGLAS C 
Published: April 2009

AbstractDNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. In this preliminary study, we tested the efficacy of a 615‐bp fragment of the cytochromecoxidase I (COI) as a DNA barcode in the medically important family Simuliidae, or black flies. A total of 65 (25%) morphologically distinct species and sibling species in species complexes of the 255 recognized Nearctic black fly species were used to create a preliminary barcode profile for the family. Genetic divergence among congeners averaged 14.93% (range 2.83–15.33%), whereas intraspecific genetic divergence between morphologically distinct species averaged 0.72% (range 0–3.84%). DNA barcodes correctly identified nearly 100% of the morphologically distinct species (87% of the total sampled taxa), whereas in species complexes (13% of the sampled taxa) maximum values of divergence were comparatively higher (max. 4.58–6.5%), indicating cryptic diversity. The existence of sibling species inProsimulium travisiandP. neomacropygawas also demonstrated, thus confirming previous cytological evidence about the existence of such cryptic diversity in these two taxa. We conclude that DNA barcoding is an effective method for species identification and discovery of cryptic diversity in black flies.
DNA barcoding reveals overlooked marine fishes
Authors: ZEMLAK TYLER S. , WARD ROBERT D. , CONNELL ALLAN D. , HOLMES BRONWYN H. , HEBERT PAUL D. N. 
Published: April 2009

AbstractWith more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most large‐bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep divergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep divergences, detected within certain inshore and inshore/offshore taxa, are typical of divergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species diversity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.
Countering criticisms of single mitochondrial DNA gene barcoding in birds
Authors: BAKER ALLAN J. , TAVARES ERIKA SENDRA , ELBOURNE REBECCA F. 
Published: April 2009

AbstractGeneral criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species‐delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within‐species and among‐species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent‐based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within‐species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene.
Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databases
Authors: ZAHARIEV M. , DAHL V. , CHEN W. , LÉVESQUE C. A. 
Published: April 2009

AbstractEfficient design of barcode oligonucleotides can lead to significant cost reductions in the manufacturing of DNA arrays. Previous methods are based on either a preliminary alignment, which reduces their efficiency for intron‐rich regions, or on a brute force approach, not feasible for large‐scale problems or on data structures with very poor performance in the worst case. One of the algorithms we propose uses ‘oligonucleotide sorting’ for the discovery of oligonucleotide barcodes of given sizes, with good asymptotic performance. Specific barcode oligonucleotides with at least one base difference from other sequences in a database are found for each individual sequence. With another algorithm, specific oligonucleotides can also be found for groups or clades in the database, which have 100% homology for all oligonucleotide sequences within the group or clade while having differences with the rest of the data. By re‐organizing the sequences/groups in the database, oligonucleotides for different hierarchical levels can be found. The oligonucleotides or polymorphism locations identified as species or clade specific by the new algorithm are refined and screened further for hybridization thermodynamic properties with third party software.
Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?
Authors: FAZEKAS ARON J. , KESANAKURTI PRASAD R. , BURGESS KEVIN S. , PERCY DIANA M. , GRAHAM SEAN W. , BARRETT SPENCER C. H. , NEWMASTER STEVEN G. , HAJIBABAEI MEHRDAD , HUSBAND BRIAN C. 
Published: April 2009

AbstractThe ability to discriminate between species using barcoding loci has proved more difficult in plants than animals, raising the possibility that plant species boundaries are less well defined. Here, we review a selection of published barcoding data sets to compare species discrimination in plants vs. animals. Although the use of different genetic markers, analytical methods and depths of taxon sampling may complicate comparisons, our results using common metrics demonstrate that the number of species supported as monophyletic using barcoding markers is higher in animals (> 90%) than plants (~70%), even after controlling for the amount of parsimony‐informative information per species. This suggests that more than a simple lack of variability limits species discrimination in plants. Both animal and plant species pairs have variable size gaps between intra‐ and interspecific genetic distances, but animal species tend to have larger gaps than plants, even in relatively densely sampled genera. An analysis of 12 plant genera suggests that hybridization contributes significantly to variation in genetic discontinuity in plants. Barcoding success may be improved in some plant groups by careful choice of markers and appropriate sampling; however, overall fine‐scale species discrimination in plants relative to animals may be inherently more difficult because of greater levels of gene‐tree paraphyly.