bluuebunny/crossref_metadata_2025 huggingface dataset:
Lactobacillus hayakitensis, L. equigenerosi and L. equi, predominant lactobacilli in the intestinal flora of healthy thoroughbreds
Authors: MORITA Hidetoshi , NAKANO Akiyo , SHIMAZU Mitsuharu , TOH Hidehiro , NAKAJIMA Fumihiko , NAGAYAMA Masahiro , HISAMATSU Shin , KATO Yukio , TAKAGI Misako , TAKAMI Hideto , AKITA Hiroaki , MATSUMOTO Minoru , MASAOKA Toshio , MURAKAMI Masaru
Published: April 2009

To detect the predominant lactobacilli in the intestinal flora of healthy thoroughbreds, we isolated lactobacilli from the feces of nine thoroughbreds (five males and four females; 0–15‐year‐old). The isolated lactobacilli comprise 17 species (37 strains), and they were classified into five groups: Lactobacillus salivarius (6 species), L. reuteri (6 species), Lactobacillus delbrueckii (3 species), L. buchneri (1 species) and L. vitulinus (1 species). On the basis of 16S rRNA gene sequences, we identified 3 other phylogenetic relatives belonging to the genus Lactobacillus. These results suggest that the intestinal flora of thoroughbreds may comprise many species of the genus Lactobacillus. Polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) analyses of the 340‐bp fragments of the 16S rRNA genes from the same nine fecal samples showed that L. hayakitensis, L. equigenerosi and L. equi are contained in all the samples, suggesting that these species are predominant lactobacilli in the intestinal flora of thoroughbreds.
Views of Intimate Partner Violence in Same‐ and Opposite‐Sex Relationships
Authors: Sorenson Susan B. , Thomas Kristie A.
Published: April 2009

Attitudes toward same‐sex intimate relationships and intimate partner violence (IPV) are changing. Little research, however, has examined norms about IPV in same‐sex relationships. Using a fractional factorial (experimental vignette) design, we conducted random‐digit‐dialed interviews in four languages with 3,679 community‐residing adults. Multivariate analyses of responses to 14,734 vignettes suggest that IPV against gay male, lesbian, and heterosexual women is more likely than that against heterosexual men to be considered illegal and that it should be illegal, police called, and a stay‐away order issued. Regardless of gender and sexual orientation, the type of abuse and whether a weapon was displayed are the strongest predictors of respondents’ judgments about whether a behavior is illegal and merits a range of societal interventions.
Which Spouse Initiates Marital Separation When There Are Children Involved?
Authors: Hewitt Belinda
Published: April 2009

This report examines whether the presence of children in marriage differentially influences the risk of wives or husbands initiating separation. The analytic sample consists of 9,118 first marriages from the Households, Income and Labour Dynamics in Australia survey (2001). Using event history and competing risks analysis, I find weak evidence that wives are less likely than husbands to initiate when they have infants, and husbands are less likely than wives to initiate when children are school age or older. Overall, the results show that children deter marital separation for both wives and husbands, indicating that gender differences in the decision to separate are likely attributable to other factors such as a willingness to remain in an unhappy marriage.
Change in the Association Between Premarital Cohabitation and Separation, Australia 1945 – 2000
Authors: Hewitt Belinda , De Vaus David
Published: April 2009

We investigate change in the association between premarital cohabitation and the risk of separation. Using retrospective marriage history data from the first wave (2001) of the Household Income and Labor Dynamics in Australian survey, we examine 6,210 first marriages formed between 1945 and 2000. We find the association between premarital cohabitation and separation is changing. The increased risk of separation for cohabitors compared to noncohabitors diminishes each year for marriages before 1988. This association then reverses for marriages after 1988, where noncohabitors have an increased risk of separation. Our results indicate that, for more recent marriages, premarital cohabitation reduces the risk of separation; more research is needed to understand the underlying mechanisms for this reversal.
Social Background Differences in Early Family Behavior
Authors: Schoen Robert , Landale Nancy S. , Daniels Kimberly , Cheng Yen‐Hsin Alice
Published: April 2009

Social background has historically been recognized as a major factor influencing family behavior, though recent work has largely emphasized racial/ethnic influences. Here we use 1994 – 1995 and 2001 – 2002 Add Health data to examine the cohabitation, first marriage, and first birth experience of young women. In a multistate life table context, hypothetical cohorts specified in terms of race and mother’s education are followed, from age 11 to age 24, as they move through 6 family‐related statuses. The results indicate that, for both Black and White women, a higher level of maternal education is generally associated with less cohabitation, less marriage, fewer first births, and a higher percentage of women who experience none of those transitions before age 24. Racial and social background differences are conceptually and empirically distinct. Because mother’s education is associated with substantially different trajectories of early family behavior for both Blacks and Whites, we argue that social background merits increased attention in research on contemporary American family patterns.
Marital Aspirations, Sexual Behaviors, and HIV/AIDS in Rural Malawi
Authors: Clark Shelley , Poulin Michelle , Kohler Hans‐Peter
Published: April 2009

We explore how marital aspirations are related to the sexual behaviors of adolescents and young adults in Malawi, where HIV/AIDS prevalence among adults exceeds 10%. We also consider whether the specter of AIDS is shaping ideals about marriage. By combining survey data (N = 1,087) and in‐depth interviews (N = 133) with young Malawians from the Malawi Diffusion and Ideational Change Project, we show that looking for and finding a suitable spouse are linked to sexual behaviors and, thus, HIV risks. Moreover, concerns about contracting HIV are closely tied to the ideal characteristics of a future spouse. Our findings draw long‐overdue attention to the importance of marital aspirations in understanding adolescent sexual behaviors and risks in the era of AIDS.
A New Look at Family Migration and Women’s Employment Status
Authors: Boyle Paul , Feng Zhiqiang , Gayle Vernon
Published: April 2009

Family migration has a negative impact on women’s employment status. Using longitudinal data from the British Household Panel Survey (3,617 women; 22,354 women/wave observations) we consider two neglected issues. First, instead of relying on the distance moved to distinguish employment‐related migrations, we use information on the reason for moving, allowing us to separate employment‐related moves, stimulated by the man or the woman, from other moves. Second, we consider selection effects and the role of state dependence in relation to women’s employment status prior to moving. Moving for the sake of the man’s job has a significant negative effect on subsequent employment status for previously employed women. Women who were not employed previously benefited only slightly from family migration.
Site‐directed mutagenesis, kinetic and inhibition studies of aspartate ammonia lyase from Bacillus sp. YM55‐1
Authors: Puthan Veetil Vinod , Raj Hans , Quax Wim J. , Janssen Dick B. , Poelarends Gerrit J.
Published: April 2009

Aspartate ammonia lyases (also referred to as aspartases) catalyze the reversible deamination of l‐aspartate to yield fumarate and ammonia. In the proposed mechanism for these enzymes, an active site base abstracts a proton from C3 of l‐aspartate to form an enzyme‐stabilized enediolate intermediate. Ketonization of this intermediate eliminates ammonia and yields the product, fumarate. Although two crystal structures of aspartases have been determined, details of the catalytic mechanism have not yet been elucidated. In the present study, eight active site residues (Thr101, Ser140, Thr141, Asn142, Thr187, His188, Lys324 and Asn326) were mutated in the structurally characterized aspartase (AspB) from Bacillus sp. YM55‐1. On the basis of a model of the complex in which l‐aspartate was docked manually into the active site of AspB, the residues responsible for binding the amino group of l‐aspartate were predicted to be Thr101, Asn142 and His188. This postulate is supported by the mutagenesis studies: mutations at these positions resulted in mutant enzymes with reduced activity and significant increases in the Km for l‐aspartate. Studies of the pH dependence of the kinetic parameters of AspB revealed that a basic group with a pKa of approximately 7 and an acidic group with a pKa of approximately 10 are essential for catalysis. His188 does not play the typical role of active site base or acid because the H188A mutant retained significant activity and displayed an unchanged pH‐rate profile compared to that of wild‐type AspB. Mutation of Ser140 and Thr141 and kinetic analysis of the mutant enzymes revealed that these residues are most likely involved in substrate binding and in stabilizing the enediolate intermediate. Mutagenesis studies corroborate the essential role of Lys324 because all mutations at this position resulted in mutant enzymes that were completely inactive. The substrate‐binding model and kinetic analysis of mutant enzymes suggest that Thr187 and Asn326 assist Lys324 in binding the C1 carboxylate group of the substrate. A catalytic mechanism for AspB is presented that accounts for the observed properties of the mutant enzymes. Several features of the mechanism that are also found in related enzymes are discussed in detail and may help to define a common substrate binding mode for the lyases in the aspartase/fumarase superfamily.
A new apparent quasar pair: Q2225-403A,B
Authors: Decarli R. , Treves A. , Falomo R.
Published: April 2009

We report the serendipitous discovery of a previously unknown quasar at 10.5 arcsec from Q2225-403 (z= 2.410). The observation of the broad emission line of Mgiiλ2798 and of the surrounding Feii multiplets indicates that the companion quasar is at z= 0.932. The spectrum of Q2225-403 shows a number of absorption lines, the most noteworthy is the Mgii line at the same redshift of the companion, suggesting that we are probing the gas within the halo ∼80 kpc from the closer quasar. From high-resolution near-infrared images, we were able to resolve the host galaxies of the two quasars. Basing on the known surface density of quasars in the 2dF survey, we estimate that the probability of finding such a close pair is ≲1 per cent.
SAXJ1808.4−3658: high-resolution spectroscopy and decrease of pulsed fraction at low energies
Authors: Patruno Alessandro , Rea Nanda , Altamirano Diego , Linares Manuel , Wijnands R. , Van Der Klis M.
Published: April 2009

XMM–Newton observed the accreting millisecond pulsar SAX J1808.4−3658 during its 2008 outburst. We present timing and spectral analyses of this observation, in particular the first pulse profile study below 2keV, and the high-resolution spectral analysis of this source during the outburst. Combined spectral and pulse profile analyses suggest the presence of a strong unpulsed source below 2keV that strongly reduces the pulsed fraction and a hard pulsed component that generates markedly double peaked profiles at higher energies. We also studied the high-resolution grating spectrum of SAX J1808.4−3658, and found several absorption edges and oxygen absorption lines with whom we infer, in a model independent way, the interstellar column densities of several elements in the direction of SAX J1808.4−3658.
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

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 APPLICATIONS

Microwave‐, 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.
Effects of Salt, BHA/BHT, and Differing Phosphate Types on Quality and Sensory Characteristics of Beef Longissimus Muscles
Authors: Rowe C.W. , Pohlman F.W. , Brown A.H. , Baublits R.T. , Johnson Z.B.
Published: April 2009

ABSTRACT:  USDA Select striploins (n = 20) were cut into thirds (anterior, medial, and posterior) and randomly assigned to 1 of 6 treatments. Treatments included: (1) control (C); (2) 0.006% BHA (butylated hydroxyl anisole)/BHT (butylated hydroxytoluene) (70%/30%) (BB); (3) 0.4% trisodiumphosphate (CT); (4) 0.4% sodiumtripolyphosphate with 0.5% salt (BH); (5) sodiumtripolyphosphate, 0.5% salt, and 0.006% BHA/BHT (70%/30%) (SB); (6) 0.2% sodiumtripolyphosphate, 0.2% trisodiumphosphate, and 0.5% salt (STB). Muscle sections were injected to 110% (10% pump) of their weight with their respective treatments. Inclusion of BHA/BHT allowed for lower mean oxidation values. Regardless of phosphate type, muscles treated with both phosphate and salt had lower retail purge (P < 0.05). Sensory panelists rated (P < 0.05) STB, SB, and BH to be juicier than all other treatments. These data suggest that inclusion of both salt and phosphate can enhance palatability, lower cook loss, and retail purge.
Quality counts: new parameters in blood cell counting
Authors: BRIGGS C.
Published: April 2009

Recently 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

Although 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

As 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

Our 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

Marine 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

The 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

DNA 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

Close 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

DNA 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

With 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

General 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

Efficient 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

The 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.
Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach
Authors: WONG EUGENE H.‐K. , SHIVJI MAHMOOD S. , HANNER ROBERT H.
Published: April 2009

Shark fisheries worldwide are mostly unmanaged, but the burgeoning shark fin industry in the last few decades has made monitoring catch and trade of these animals critical. As a tool for molecular species identification, DNA barcoding offers significant potential. However, the genetic distance‐based approach towards species identification employed by the Barcode of Life Data Systems may oftentimes lack the specificity needed for regulatory or legal applications that require unambiguous identification results. This is because such specificity is not typically realized by anything less than a 100% match of the query sequence to an entry in the reference database using genetic distance. Although various divergence thresholds have been proposed to define acceptable levels of intraspecific variation, enough exceptions exist to cast reasonable doubt on many less than exact matches using a distance‐based approach for the identification of unknowns. An alternative approach relies on the identification of discrete molecular characters that can be used to unambiguously diagnose species. The objective of this study was to assess the performance differences between these competing approaches by examining more than 1000 DNA barcodes representing nearly 20% of all known elasmobranch species. Our results demonstrate that a character‐based, nucleotide diagnostic (ND) approach to barcode identification is feasible and also provides novel insights into the structure of haplotype diversity among closely related species of sharks. Considerations for the use of NDs in applied fields are also explored.
Retinal artery occlusion following intravitreal anti‐VEGF therapy
Authors: Von Hanno Therese , Kinge Bettina , Fossen Kristian
Published: April 2009

Purpose:  Anti‐vascular endothelial growth factor (anti‐VEGF) therapy effectively inhibits angiogenesis and is now enjoying widespread use in the treatment of age‐related macular degeneration (AMD). It may also have a role in the treatment of macular oedema secondary to other conditions. VEGF is a signalling molecule that has a variety of roles, including vasoregulation and effects on the coagulation homeostasis. Anti‐VEGF therapy may therefore have adverse effects on ocular blood flow.

Methods:  Two cases of retinal artery occlusion after intravitreal injection of anti‐VEGF are presented. Both patients were given the treatment to reduce macular oedema secondary to central retinal vein occlusion. Possible mechanisms are discussed.

Results:  Patient 1 developed a central retinal artery occlusion within 1 month of an intravitreal injection of ranibizumab (Lucentis®). The macular oedema was totally resolved at 1 month; final visual acuity (VA) was light perception. Patient 2 developed a branch retinal artery occlusion in the macula 2 days after an intravitreal injection of bevacizumab (Avastin®). The macular oedema was almost resolved within 1 week and did not recur; final VA was 0.6.

Conclusions:  Anti‐VEGF therapy may have a role in the treatment of macular oedema caused by central retinal vein occlusions. However, our report indicates that the therapeutic principle may be associated with an increased risk of retinal arterial occlusions.
New Fossils of Eoptychopteridae (Diptera) from the Middle Jurassic of Northeastern China
Authors: HAO Jianying , REN Dong , SHIH Chungkun
Published: April 2009

Three new species of the extinct genus of Eoptychopterina from the Eoptychopteridae family, Eoptychopterina antica sp. nov., Eoptychopterina adnexa sp. nov., and Eoptychopterina mediata sp. nov., are described and illustrated. These three new species are established based on fossil specimens with bodies and complete wings. All were collected from the Middle Jurassic Jiulongshan Formation of Daohugou in eastern Inner Mongolia, China. Based on the new materials, the name of two species in Eoptychopterina from China—Eoptychopterina elenae Ren and Krzeminski and Eoptychopterina gigantea Zhang—is sysnonymum Junius.
A New Basal Neoceratopsian Dinosaur from the Middle Cretaceous of Jilin Province, China
Authors: JIN Liyong , CHEN Jun , ZAN Shuqin , GODEFROIT Pascal
Published: April 2009

A new basal neoceratopsian dinosaur, Helioceratops brachygnathus gen. et sp. nov., is described from the Quantou Formation (late Early Cretaceous or early Late Cretaceous) in the Liufangzi locality (Jilin province, China). Helioceratops differs from other basal neoceratopsians with its deep dentary ramus, its steeply‐inclined ventral predentary facet, its heterogeneous dentary crowns, and by the denticles and secondary ridges asymmetrically distributed on either side of the primary ridge on its dentary teeth. Along with Auroraceratops and Yamaceratops, Helioceratops represents one of the most derived non‐coronosaurian neoceratopsians. The palaeogeographical distribution of basal neoceratopsians appears limited to northern China and southern Mongolia in the current state of our knowledge. It is therefore probable that this region constituted the birthplace for more advanced, Late Cretaceous Coronosauria.
Carbon and Oxygen Isotopic Composition of Surface‐Sediment Carbonate in Bosten Lake (Xinjiang, China) and its Controlling Factors
Authors: ZHANG Chengjun , MISCHKE Steffen , ZHENG Mianping , PROKOPENKO Alexander , GUO Fangqin , FENG Zhaodong
Published: April 2009

Bosten Lake is a mid‐latitude lake with water mainly supplied by melting ice and snow in the Tianshan Mountains. The depositional environment of the lake is spatially not uniform due to the proximity of the major inlet and the single outlet in the western part of the lake. The analytical results show that the carbon and oxygen isotopic composition of recent lake sediments is related to this specific lacustrine depositional environment and to the resulting carbonate mineralogy. In the southwestern lake region between the Kaidu River inlet and the Kongqi River outlet, carbon isotope composition (δ13C) values of the carbonate sediment (−1‰ to −2‰) have no relation to the oxygen isotope composition of the carbonate (δ18O) values (−7‰ to –8‰), with both isotopes showing a low variability. The carbonate content is low (<20%). Carbonate minerals analyzed by X‐ray diffraction are mainly composed of calcite, while aragonite was not recorded. The salinity of the lake water is low in the estuary region as a result of the Kaidu River inflow. In comparison, the carbon and oxygen isotope values are higher in the middle and eastern parts of the lake, with δ13C values between approximately +0.5‰ and +3‰, and δ18O values between −1‰ and −5‰. There is a moderate correlation between the stable oxygen and carbon isotopes, with a coefficient of correlation r of approximately 0.63. This implies that the lake water has a relatively short residence time. Carbonate minerals constitute calcite and aragonite in the middle and eastern region of the lake. Aragonite and Mg–calcite are formed at higher lake water salinity and temperatures, and larger evaporation effects. More saline lake water in the middle and eastern region of the lake and the enhanced isotopic equilibrium between water and atmospheric CO2 cause the correlating carbon and oxygen isotope values determined for aragonite and Mg–calcite. Evaporation and biological processes are the main reasons for the salinity and carbonate mineralogy influence of the surface‐sediment carbonate in Bosten Lake. The lake water residence time and the CO2 exchange between the atmosphere and the water body control the carbon and oxygen isotope composition of the carbonate sediment. In addition, organic matter pollution and decomposition result in the abnormally low carbon isotope values of the lake surface‐sediment carbonate.
Late Jurassic–Early Cretaceous Plutonism in the Northern Part of the Precambrian North China Craton: SHRIMP Zircon U–Pb Dating of Diorites and Granites from the Yunmengshan Geopark, Beijing
Authors: SHI Yuruo , ZHAO Xitao , MA Yinsheng , HU Daogong , LIU Qisheng , WU Zhenhan , ZHAO Yuanyi , LIU Dunyi
Published: April 2009

The Yunmengshan Geopark in northern Beijing is located within the Yanshan range. It contains the Yunmengshan batholith, which is dominated by two plutons: the Yunmengshan gneissic granite and the Shicheng gneissic diorite. Four samples of the Yunmengshan gneissic granite give SHRIMP zircon U–Pb ages from 145 to 141 Ma, whereas four samples of the Shicheng gneissic diorite have ages from 159 Ma to 151 Ma. Dikes that cut the Yunmengshan diorite record SHRIMP zircon U–Pb age of 162±2 and 156±4 Ma. The cumulative plots of zircons from the diorites show a peak age of 155 Ma, without inherited zircon cores, and the peak age of 142 Ma for granite is interpreted as the emplacement age of the Yunmengshan granitic pluton, whose igneous zircons contain inherited zircon cores. The data presented here show that there were two pulses of magmatism: early diorites, followed c13 Ma later by true granites, which incorporated material from an older continental crust.
A New Species of Gobiconodon (Mammalia) from Western Liaoning, China and its Implication for the Dental Formula of Gobiconodon
Authors: YUAN Chongxi , XU Li , ZHANG Xingliao , XI Yunhong , WU Yanhua , JI Qiang
Published: April 2009

A new species of Gobiconodon from the Early Cretaceous in the Lujiatun locality of western Liaoning is erected based on an almost complete skull and lower jaw. It has a flatten skull roof, the lambdoidal crest is strongly curved forward, and the sagittal crest is short and low. There is a protuberance near the anterior base of the zygoma. The preservation of the upper teeth is very rare in all known Gobiconodon, and this provides important information for the study on the formula of Gobiconodon. The new species is the fifth primitive mammal unearthed from the Lujiatun locality, and is of great value for the study of the geological age of the stratigraphy at Lujiatun by primitive mammal material.
Comparison of the Typical Metallogenic Systems in the North Slope of the Tongbai‐East Qinling Mountains and its Geologic Implications
Authors: ZHANG Jing , CHEN Yanjing , QI Jinping , GE Jun
Published: April 2009

The Tongbai‐East Qinling Mountains, an important part of the Central orogenic belt, is one of the most important metallogenic belts in China and contains lots of orogenic‐type and VMS‐type (Volcanogenic Massive Sulfide type) metallogenic systems. The Dahe and Shuidongling VMS‐type Cu‐Zn deposits, located in the Erlangping Group in Tongbai and East Qinling Mountains, respectively, show similar geological and geochemical features. The Huoshenmiao Formation in the East Qinling region and the Liushanyan Formation in the Tongbai region are spilite‐keratophyre sequences occurring in the western and eastern sides of the Nanyang Basin, respectively, and are interpreted to be equivalent to each other. The orogenic‐type Au‐Ag deposits can be subdivided into two styles; namely, fault‐ or structure‐controlled (e.g. Yindonggou) and stratabound (e.g. Poshan). The Poshan and Yindongpo orogenic‐type Au‐Ag deposits, whose ore bodies are strictly hosted in carbonaceous strata in the Tongbai Mountains, show obvious stratabound characteristics. Their ore‐fluids are enriched in K+ and SO2−4 and are regarded as K+‐SO2−4 types. The Pb‐isotope ratios of sulfides of the ores are extremely uniform and significantly different from those of the tectonostratigraphic terranes of the Qinling orogens except for the ore‐hosting strata of the Waitoushan Formation. The Yindonggou and Xuyaogou orogenic Au‐Ag deposits in the East Qinling Mountains, whose ore bodies are hosted in the faults cutting the hosting strata or granite body, show fault‐controlled characteristics. Their ore‐fluids belong to the Na+‐Cl− type. The Pb‐isotope ratios of sulfides of ores are similar to those of the northern Qinling orogenic belt. The Waitoushan Formation, dominated by carbonaceous sericite‐rich schists and only occurring in Tongbai region, should be detached from the Erlangping Group, which occurs both in the western and eastern sides of the Nanyang Basin. Future ore exploration in the Tongbai‐East Qinling Mountains should focus on fault‐controlled Au‐Ag lodes.