bluuebunny/crossref_metadata_2025_split huggingface dataset:
DETERMINATION OF OIL POINT PRESSURE FOR MELON SEEDS
Authors: TUNDE‐AKINTUNDE T.Y. 
Published: April 2009

ABSTRACT The oil point pressure of melon seed oil at different processing conditions, i.e., preheating moisture content (6.6, 8.3, 10.0 and 12.0% wet basis [w.b.]), heating temperature (70, 85, 100 and 115C) and heating time (15, 20, 25 and 30 min), was determined. The postheating moisture content increased with an increase in preheating moisture content and decrease in heating temperature and time. The oil point pressure obtained varied from 0.84 MPa for a moisture content of 6.6% (w.b.) heated for 30 min at 100C to 2.05 MPa for a moisture content of 12.0% (w.b.) heated for 15 min at 70C. The oil point pressure increased with increase in preheating moisture content and decreased as the heating temperature and time increased from 70 to 100C and from 15 to 25 min, respectively. A further increase in heating temperature to 115C and heating time to 30 min, however, increased the oil point. PRACTICAL APPLICATIONSMelon seeds are one of the commonly available oilseeds with a high oil content, and their high oil content makes them valuable for oil production. The optimization of the expression process through the identification of the oil point pressure of melon seeds is necessary for the effectiveness/efficiency of the process. The maximum oil point pressure (2.05 MPa) was obtained from the lowest value of heating temperature (70C) and time (15 min) and the highest moisture content (12.0% wet basis), while the minimum value (0.84 MPa) was from high heating temperatures and time and the lowest preheating moisture content. These indicate that reduced heat treatment of melon seeds increases the pressure required for expression, thus reducing process efficiency and increasing production cost.
Rove beetles (Coleoptera: Staphylinidae) in Neotropical riverine landscapes: characterising their distribution
Authors: GUTIÉRREZ‐CHACON CATALINA , ZÚÑIGA MARIA DEL CARMEN , VAN BODEGOM PETER MICHIEL , CHARÁ JULIÁN , GIRALDO LINA PAOLA 
Published: April 2009

Abstract. The diversity and ecology of Staphylinidae in the Neotropical region has been poorly investigated, especially in riverine landscapes where these beetles are among the dominant organisms. Therefore, the relation between the occurrence of Staphylinidae and environmental variables was investigated in riverine systems of Southwest and Central Colombia.Samples were collected between 1984 and 2006 following standardised methods for biological sampling and water quality evaluation. Water quality indexes were calculated and six microhabitats were surveyed: riparian vegetation (light traps), sediments (surber net), rock, macrophytes and litter (manually).The 1834 collected individuals belonged to seven subfamilies and 17 genera. The most frequent genera wereThinodromus, StenusandPhilonthus.Among all measured environmental variables, microhabitat explained to most extent the distribution patterns of the rove beetles. Preference to riparian vegetation was found for the family as a whole but preferences by subfamilies differed strongly. Steninae were absent in the riparian vegetation and showed close association to macrophytes. Oxytelinae and Staphylininae were frequently collected in riparian vegetation and litter, respectively. Although water quality and altitude were only of secondary importance to the Staphylinidae distribution, the tolerance of Steninae to waters of poorer quality and its concentration in the altitudinal range of 1001–1500 m a.s.l. is highlighted.Preferences to certain microhabitats found for some Staphylinidae taxa supply more evidence to the habitat‐specialisation of these beetles, representing an important contribution to both their ecological characterisation and to the fauna of riverine systems in the Neotropical region.
Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity
Authors: JANZEN DANIEL H. , HALLWACHS WINNIE , BLANDIN PATRICK , BURNS JOHN M. , CADIOU JEAN‐MARIE , CHACON ISIDRO , DAPKEY TANYA , DEANS ANDREW R. , EPSTEIN MARC E. , ESPINOZA BERNARDO , FRANCLEMONT JOHN G. , HABER WILLIAM A. , HAJIBABAEI MEHRDAD , HALL JASON P. W. , HEBERT PAUL D. N. , GAULD IAN D. , HARVEY DONALD J. , HAUSMANN AXEL , KITCHING IAN J. , LAFONTAINE DON , LANDRY JEAN‐FRANÇOIS , LEMAIRE CLAUDE , MILLER JACQUELINE Y. , MILLER JAMES S. , MILLER LEE , MILLER SCOTT E , MONTERO JOSE , MUNROE EUGENE , GREEN SUZANNE RAB , RATNASINGHAM SUJEEVAN , RAWLINS JOHN E. , ROBBINS ROBERT K. , RODRIGUEZ JOSEPHINE J. , ROUGERIE RODOLPHE , SHARKEY MICHAEL J. , SMITH M. ALEX , SOLIS M. ALMA , SULLIVAN J. BOLLING , THIAUCOURT PAUL , WAHL DAVID B. , WELLER SUSAN J. , WHITFIELD JAMES B. , WILLMOTT KEITH R. , WOOD D. MONTY , WOODLEY NORMAN E. , WILSON JOHN J. 
Published: April 2009

AbstractInventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0–2000 m elevation contains at least 10 000 species of non‐leaf‐mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG‐reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co‐authors. DNA barcoding — the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species — was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to ‘variation’ or thought to be insignificant for species‐level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
The front‐end logistics of DNA barcoding: challenges and prospects
Authors: BORISENKO ALEX V. , SONES JAYME E. , HEBERT PAUL D. N. 
Published: April 2009

AbstractBuilding a global library of DNA barcodes will require efficient logistics of pre‐laboratory specimen processing and seamless interfacing with molecular protocols. If not addressed properly, the task of aggregating specimens may become the biggest bottleneck in the analytical chain. Three years of experience in developing a collection management system to facilitate high‐throughput DNA barcoding have allowed the Canadian Centre for DNA Barcoding to recognize and resolve the most common logistical obstacles. Dealing with these challenges on a larger scale will be an important step towards building a solid collection‐based foundation for the international DNA barcoding effort.
DNA barcoding and the mediocrity of morphology
Authors: PACKER LAURENCE , GIBBS JASON , SHEFFIELD CORY , HANNER ROBERT 
Published: April 2009

AbstractA small but vocal community of critics has questioned the epistemological value of DNA barcoding by suggesting that either it ‘cannot work’ for the identification or discovery of species or that it ignores the ‘richness’ inherent in traditional approaches. We re‐examine these arguments through a comparison of DNA barcoding and morphological taxonomy in terms of their accuracy and diversity of characters employed. We conclude that morphology often does not work and that it is often nowhere near as ‘rich’ as has been argued. Morphology is particularly poor in numerous important situations, such as the association of larvae with adults and discrimination among cryptic species. The vehemence of some of the criticisms is surprising given that morphology alone is known to be inadequate to the task of species‐level identification in many instances.
Biological agent detection technologies
Authors: JAKUPCIAK JOHN P. , COLWELL RITA R. 
Published: April 2009

AbstractThe challenge for first responders, physicians in the emergency room, public health personnel, as well as for food manufacturers, distributors and retailers is accurate and reliable identification of pathogenic agents and their corresponding diseases. This is the weakest point in biological agent detection capability today.There is intense research for new molecular detection technologies that could be used for very accurate detection of pathogens that would be a concern to first responders. These include the need for sensors for multiple applications as varied as understanding the ecology of pathogenic micro‐organisms, forensics, environmental sampling for detect‐to‐treat applications, biological sensors for ‘detect to warn’ in infrastructure protection, responses to reports of ‘suspicious powders’, and customs and borders enforcement, to cite a few examples.The benefits of accurate detection include saving millions of dollars annually by reducing disruption of the workforce and the national economy and improving delivery of correct countermeasures to those who are most in need of the information to provide protective and/or response measures.
Barcoding diatoms: Is there a good marker?
Authors: MONIZ MÓNICA B. J. , KACZMARSKA IRENA 
Published: April 2009

AbstractThe promise of DNA barcoding is based on a small DNA fragment divergence coinciding with biological species separation. Here we evaluated the performance of three markers as diatom barcodes, the small ribosomal subunit (1600 bp), a 5′ end fragment of cytochromecoxidase subunit 1 (430 bp), and the second internal transcribed spacer region combined with the 5.8S gene (5.8S + ITS‐2, 300–400 bp). Forty‐four sequences per marker representing 28 species from all diatom classes were analysed. Sequence alignment of the three genetic markers and uncorrected genetic distances (P) were calculated at the intra‐ and heterospecific level. All three markers correctly separated the species examined and had advantages which contribute to their feasibility as a DNA barcode. Small ribosomal subunit had the largest GenBank data set, its success rate in amplification and sequencing was assumed to be the highest of all three and was readily aligned. However, it required a long fragment to recover divergence sufficient for species separation and small genetic distances increased the potential for misidentifications. Cytochromecoxidase subunit 1 demonstrated a substantial heterospecific divergence level and was also readily alignable, but it showed very low amplification and sequencing success rates with currently existing primers. 5.8S + ITS‐2 was amplified and sequenced with high success rate and was the most variable of the three markers, but its secondary structure was needed to aid in alignment. However, since it has been recently suggested that ITS‐2 may provide insight into sexual compatibility, this marker offers an additional advantage. We therefore propose that the 5.8S + ITS‐2 fragment is the best candidate as a diatom DNA barcode.
Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths
Authors: MOSZCZYNSKA ANNA , LOCKE SEAN A. , McLAUGHLIN J. DANIEL , MARCOGLIESE DAVID J. , CREASE TERESA J. 
Published: April 2009

AbstractThe phylum Platyhelminthes is a diverse group of flatworms that includes parasites with serious impacts on human health, animal husbandry, aquaculture and wildlife management. Here we present degenerate primers for the barcode region of the mitochondrial cytochrome c oxidase I (COI) gene in flatworms. Although amplicons were obtained from a wide taxonomic range in the Cestoda and Trematoda, COI fragments from many taxa in these classes did not amplify. Primers specific to trematodes in the family Diplostomidae were also developed. Amplification success was much higher with diplostomid‐specific primers and sequences were obtained from 504 of 585 specimens of Diplostomum and Tylodelphys. Sequences from the barcode region resolved all specimens to the species level, with mean divergence between congeners of 19% (3.9–25%). Because many of our specimens were small, we initially amplified part of the nuclear small subunit ribosomal (r) RNA gene to evaluate the quality and quantity of DNA in our specimens. Short sequences (~380 nt) of this gene were recovered from most specimens and can be used to distinguish specimens at the family level and often the generic level. We suggest that rRNA genes could be used to screen samples of completely unknown taxonomy, after which specific COI primers could be used to obtain species‐level identifications.
Progress towards DNA barcoding of fungi
Authors: SEIFERT KEITH A. 
Published: April 2009

AbstractThe use of DNA sequences for identifying fungi and fungus‐like organisms predates the DNA barcoding movement by at least 10 years. A brief overview of the mycological shift from phenotypic to molecular taxonomy is provided. Exploration of the animal barcode marker, cytochrome oxidase 1, by Canadian mycologists has been fruitful for some fungi, but intron issues and lack of resolution in other taxa prevent its universal application. The momentum established by 15 years of research on the fungal nuclear ribosomal internal transcribed spacer (ITS) sequences will lead to a proposal to the Consortium for the Barcode of Life on the adoption of this marker as the fungal barcode. Existing mycological research networks should facilitate the rapid development of DNA barcoding of fungi once the marker issue is settled. Some available online fungal identification databases are briefly described.
Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium
Authors: GILMORE SCOTT R. , GRÄFENHAN TOM , LOUIS‐SEIZE GERRY , SEIFERT KEITH A. 
Published: April 2009

AbstractUsing data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1‐based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences.
Evaluation of mitochondrial genes as DNA barcode for Basidiomycota
Authors: VIALLE AGATHE , FEAU NICOLAS , ALLAIRE MATHIEU , DIDUKH MARYNA , MARTIN FRANCIS , MONCALVO JEAN‐MARC , HAMELIN RICHARD C. 
Published: April 2009

AbstractOur study evaluated in silico the potential of 14 mitochondrial genes encoding the subunits of the respiratory chain complexes, including cytochrome c oxidase I (CO1), as Basidiomycota DNA barcode. Fifteen complete and partial mitochondrial genomes were recovered and characterized in this study. Mitochondrial genes showed high values of molecular divergence, indicating a potential for the resolution of lower‐level relationships. However, numerous introns occurred in CO1 as well as in six other genes, potentially interfering with polymerase chain reaction amplification. Considering these results and given the minimal length of 600‐bp that is optimal for a fungal barcode, the genes encoding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH dehydrogenase subunit 6 have the most promising characteristics for DNA barcoding among the mitochondrial genes studied. However, biological validation on two fungal data sets indicated that no single mitochondrial gene gave a better taxonomic resolution than the ITS, the region already widely used in fungal taxonomy.
Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)
Authors: STARR JULIAN R. , NACZI ROBERT F. C. , CHOUINARD BRIANNA N. 
Published: April 2009

AbstractWe investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH‐psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best‐known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH‐psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50–60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0–13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH‐psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system. Although identification rates in this study are low, they can be significantly improved by a regional approach to barcoding.
Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae)
Authors: STEVEN G. NEWMASTER , SUBRAMANYAM RAGUPATHY 
Published: April 2009

Abstract Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister‐species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH‐psbA and matK). Our results show that all three regions (rbcL, matK and trnH‐psbA) can distinguish and support the newly proposed genera of Vachellia Wight & Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.
DNA barcode accumulation curves for understudied taxa and areas
Authors: SMITH M. ALEX , FERNANDEZ‐TRIANA JOSE , ROUGHLEY ROB , HEBERT PAUL D. N. 
Published: April 2009

AbstractFrequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well‐known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment — parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha‐taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.
Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis)
Authors: KAPHEIM KAREN M. , POLLINGER JOHN P. , WCISLO WILLIAM T. , WAYNE ROBERT K. 
Published: April 2009

AbstractWe developed a library of twelve polymorphic di‐ and tri‐nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7–20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy–Weinberg equilibrium proportions or was found to be in gametic disequilibrium.