bluuebunny/crossref_metadata_2025 huggingface dataset:
Badgers and TB – Does Gassing Spread the Disease?
Authors: Overend Eunice D.
Published: April 2009

For the past six years the Ministry of Agriculture has been tackling the problem of TB in badgers in a few areas in south-west England by gassing all infected sets and those in immediately adjoining territories as dangerous contact, with the expectation of eliminating all the infected badgers. The author points out that because TB is a stress disease, and because it is impossible to gas every badger in a group simultaneously, gassing may be driving infected individual badgers to join other groups and infect them, thus actually spreading the disease.
Why Plants Are Vital
Authors: Jarvis Charlie
Published: April 2009

Man depends on plants for his food – directly through crops and indirectly through animals – and all our staple foods are derived from only about 30 species of plants. Yet we continue to fell the forests and clear land, exterminating plants that could possibly avert disasters in the future – just as the apparently useless wild wheat discovered in Turkey in 1948 proved to be resistant to certain diseases, including four races of rust, and is now used to breed rust-resistant hydrids. The author lists some of the disasters now occurring, such as siltation of waterways resulting from erosion due to forest destruction – some bulk cargoes are now diverted round Cape Horn due to silt in the Panama Canal. He asks, how severe must ecological disasters become before we recognise our dependence? Dr Jarvis works for IUCN's Threatened Plants Committee (TPC) at the Royal Botanic Gardens, Kew.
‘Structural Interests’ in Health Care: Evidence from the Contemporary National Health Service
Authors: CHECKLAND KATH , HARRISON STEPHEN , COLEMAN ANNA
Published: May 2009

Alford's theory of structural interests has been used as a framework within which to analyse health systems across the world. However, authors have often been uncritical in their acceptance of Alford's original analytic categories. In this article we use data from a detailed qualitative study of the introduction of Practice Based Commissioning in the UK NHS to interrogate Alford's work more critically. Disrupting Alford's original categories of ‘professional monopolisers’ as dominant interests, challenged by management ‘corporate rationalisers’, we suggest that the new structures established in the NHS since 2002 systematically privilege an interest that we call ‘corporate monopolisers’, and that this is under challenge from ‘professional rationalisers’.
DISABILITY, STATUS ENHANCEMENT, PERSONAL ENHANCEMENT AND RESOURCE ALLOCATION
Authors: Wolff Jonathan
Published: May 2009

It often appears that the most appropriate form of addressing disadvantage related to disability is through policies that can be called “status enhancements”: changes to the social, cultural and material environment so that the difficulties experienced by those with impairments are reduced, even eradicated. However, status enhancements can also have their limitations. This paper compares the relative merits of policies of status enhancement and “personal enhancement”: changes to the disabled person. It then takes up the question of how to assess the priority of the claims of disabled people in the face of scarcity of resources for which there can be many competing social claims, arguing for the theory of “declustering disadvantage”.
A RESPONSE TO ERIK SCHOKKAERT ONMACROJUSTICE
Authors: Kolm Serge-Christophe
Published: May 2009

Erik Schokkaert's note presents a very good summary of the theory of macrojustice and a very good list of the directions of research it points to. This is quite fitting since a research programme defines a paradigm, and he sees this proposal as a paradigm shift. This is also very appropriate since his own qualifications are the best for advancing fast in these research topics. I have only a very small number of qualifications to add to his presentation, but I prefer to begin with emphasizing the most important issues. Two aspects can be seen as the most important: the de facto axiomatic derivation of the solution ELIE and its application on the one hand, and the present state of scholarly studies of the optimum or just distribution of income on the other hand. Let us enter by the second door (as opposed to what is done in the bookMacrojustice). This will lead us to conclude with a more synthetic and broader view of the basic logic of the paradigms of justice and of the surprising recent history of their interpretations.
Birtwistle's The Minotaur: the opera and a diary of its first production
Authors: SAMUEL RHIAN
Published: May 2009

Harrison Birtwistle's The Minotaur, to a libretto by David Harsent, was premiered at The Royal Opera House, Covent Garden, in April 2008. This article offers a synopsis, a diary of rehearsals for the opera (for all of which the composer was in attendance), and an analytical essay. The diary chronicles the development of the production, with its diversions from, and clarifications of, the text as well as the composer's reaction to these. The essay presents The Minotaur as a departure for Birtwistle, from narrative (as in the earlier Gawain) to characterisation, its basis being a trio of protagonists. While a predictably heroic Theseus and tragic Minotaur are characters fashioned by the libretto as much as the music, a multi-faceted Ariadne is primarily the composer's creation.
Lipid mobilization, gluconeogenesis and ageing-related processes in dormant walnut kernels during moist chilling and warm incubation
Authors: Nezamdoost Tahereh , Tamaskani Fatemeh , Abdolzadeh Ahmad , Sadeghipour Hamid Reza
Published: May 2009

To understand the beneficial effects of cold conditions during the alleviation of dormancy of walnut (Juglans regiaL.), lipid mobilization, gluconeogenesis and changes related to ageing were compared in dormant kernels incubated in the cold and under deteriorating warm conditions. Stratifying kernels at 5°C for 30 d enhanced their germination capacity, whereas warm-incubated (27°C) kernels turned rancid after 20 d and had reduced germination. Kernel imbibition was sufficient to bring about lipid mobilization, irrespective of temperature of incubation. Although imbibed kernels displayed high isocitrate lyase activity, starch and soluble sugar accumulation occurred only under cold conditions. Deteriorative 64 kDa fatty acyl-ester hydrolase activity declined in cold-stratified kernels. Cold treatment also led to reduced lipid peroxidation and hydrogen peroxide in kernels. The activity of NADP+-isocitrate dehydrogenase, an NADPH-generating enzyme, declined in warm-incubated kernels. Thus, warm-incubated kernels undergo ageing associated with oxidative stress, but there are beneficial effects of cold stratification in preventing deteriorative ageing-related processes. Imbibition is sufficient to allow lipid mobilization to occur in dormant walnut kernels, although cold stratification accompanied by gluconeogenesis is essential for kernel germination.
Forest seed banks along an intensity gradient of ancient agriculture
Authors: Plue J. , Dupouey J.-L. , Verheyen K. , Hermy M.
Published: May 2009

Recently, forest seed banks were proven to not only reflect former (decades-old) but also ancient (centuries-old) land use. Yet, as land-use intensity determines the magnitude of seed-bank changes in recent forests, this study aims to identify whether an ancient land-use gradient would also be reflected in the seed bank. On a forested 1600-year-old archaeological site, five different land-use intensities were mapped and sampled. Apart from seed density, species richness and composition, functional seed-bank types, defined by nine seed-bank-related plant traits, were related to the land-use intensity gradient. The land-use gradient from gardens to undisturbed sites was still clearly reflected in the soil seed bank. Six emergent functional seed-bank types, characterized by specific plant traits, changed significantly in abundance, parallel to the land-use gradient. In particular, dispersal agent (and related traits) proved an important explanatory trait of present (functional) seed-bank patterns. Poor dispersers (large and heavy seeds) were not found in the intensively used areas, contrary to animal-dispersed species. Wind-dispersers may have been inhibited in the extension of their distribution by recruitment bottlenecks (low seed production) and/or competitive exclusion. Additionally, the agricultural land-use probably introduced ruderal species into the seed bank of the most intensively used areas, yielding a simultaneous increase in vegetation–seed-bank dissimilarity with land-use intensity, eliminating present vegetation as a driver behind the differences over the seed-bank gradient. We conclude by arguing how coppice-with-standards management possibly maintained the seed-bank gradient.
Nutrition and body weights of Canadian children watching television and eating while watching television
Authors: Liang Tina , Kuhle Stefan , Veugelers Paul J
Published: May 2009

Objective

To examine whether eating while watching television poses a risk for poor nutrition and excess body weight over and above that of time spent watching television.

Design

We analysed data of grade 5 students participating in a comprehensive population-based survey in the Canadian province of Nova Scotia. This survey included the Harvard’s Youth Food Frequency Questionnaire, students’ height and weight measurements, and a parent survey. We applied multivariable linear and logistic random effects models to quantify the associations of watching television and eating while watching television with diet quality and body weight.

Setting

The province of Nova Scotia, Canada.

Subjects

Grade 5 students (n4966).

Results

Eating supper while watching television negatively affected the consumption of fruits and vegetables and overall diet quality. More frequent supper while watching television was associated with more soft drink consumption, a higher percentage energy intake from sugar out of total energy from carbohydrate, a higher percentage energy intake from fat, and a higher percentage energy intake from snack food. These associations appeared independent of time children spent watching television. Both watching television and eating while watching television were positively and independently associated with overweight.

Conclusions

Our observations suggest that both sedentary behaviours from time spent watching television as well as poor nutrition as a result of eating while watching television contribute to overweight in children. They justify current health promotion targeting time spent watching television and call for promotion of family meals as a means to avoid eating in front of the television.
Expressed sequence tag analysis and cDNA array establishment of Nicotiana tabacum: application to salinity stress
Authors: Wen-Zheng Li , Li-Min Song , Yong-Ping Li , Xiu-Ping Lu , Hong-Mei Luo , Cheng-En Dai , Yong-Qi Fang , Hai-Tao Dong , De-Bao Li
Published: April 2009

This study aimed to explore high-throughput cDNA array monitoring technology and to apply it to the gene expression spectrum analysis of salinity-challenged tobacco plants. A Nicotiana tabacum cDNA library was sequenced and found to consist of 5927 high-quality sequences (GenBank accession nos CV015900-CV021826). By analysing the expressed sequence tags (ESTs), the proportion of N. tabacum genes was identified at the EST level. A cDNA array was constructed based on the tentative unique transcripts (TUTs) derived from EST assembling results. A total of 42 differentially expressed genes were identified, including plasma membrane intrinsic protein 2a, ethylene-responsive proteinase and pre-mRNA splicing factor prp31 gene, suggesting that there was a complicated biological response in N. tabacum under saline stress.
Characterization and heterologous expression of testosterone-inducible regulator fromComamonas testosteroniinEscherichia coli
Authors: Jian-Qiu Chen , Yu-Fang Ai , Yi-Fei Zhou , Da-Ren Pan , Guang-Ming Xiong , Yu-Chun Guo , Fei Pan , Bing-Hui Lin
Published: April 2009

The testosterone-inducible regulator (teiR) gene was cloned fromComamonas testosteronichromosomal DNA, and introduced into plasmids pKtac2 (containing atacpromoter) and pK18 to yield plasmids pKtac2-teiRand pKteiR100. The recombinant plasmids were transformed into competentEscherichia coliHB101 and total protein was extracted to detect the TeiR protein expression level using enzyme-linked immunosorbent assay (ELISA).E. colitransformed by pKtac2-teiRand pKteiR100produced 6.65 and 5.93 μg/mg of TeiR protein, respectively. Recombinant plasmids were also co-transformed into competentE. coliHB101 with plasmid p6 [containinghsdAgene (3α-HSD/CR, 3α-hydroxysteroid dehydrogenase/carbonyl reductase encoding gene)] to reveal the relationship between 3α-HSD/CR and TeiR by ELISA. The amounts of TeiR protein expressed byE. colicontaining pKtac2-teiRand pKteiR100were 5.94 μg/mg and 5.33 μg/mg, respectively, and these increased up to 6.81 μg/mg and 6.10 μg/mg after inducing with 1 mmol/l isopropyl-β-d-thiogalactoside (IPTG). Interestingly, 3α-HSD/CR protein expression level, after co-transformation with plasmids pKtac2-teiRand p6, was lower than that observed in the co-transformation with pKteiR100and p6. The first co-transformation induced 1.20 μg/mg 3α-HSD/CR protein and the second 1.71 μg/mg. These values rose to 1.42 and 1.80 μg/mg, respectively, after treatment with 1 mmol/l IPTG. Our results proved that thetacpromoter was more efficient than thelacZpromoter and that theteiRgene could act as an activator forhsdAgene expression.
Expression optimization of subunitfasGof 987P fimbriae in enterotoxigenicEscherichia coli(ETEC)
Authors: He-Feng Luo , Jie Wang , Zhong-Yong Gou , Jian Peng
Published: April 2009

Four bioengineered bacteria having thefasGgene were constructed using twoEscherichia coliexpression strains (BL21 (DE3) and Rossetta (DE3)) with different tRNA profiles and twoE. coliexpression vectors (pET28a(+) and pGEX-KG) to examine the influence of rare codons on the expression of thefasGgene. The induction expression result of bioengineered bacteria showed that the expression levels of target proteins in Rossetta (DE3), which contained the tRNAs of the rare codons, were higher than in BL21 (DE3), either using pET-fasGor pKG-fasG.
Glacial‐interglacial circulation changes inferred from 231Pa/230Th sedimentary record in the North Atlantic region
Authors: Gherardi J.‐M. , Labeyrie L. , Nave S. , Francois R. , McManus J. F. , Cortijo E.
Published: May 2009

Studies from the subtropical western and eastern Atlantic Ocean, using the 231Pa/230Th ratio as a kinematic proxy for deep water circulation, provided compelling evidence for a strong link between climate and the rate of meridional overturning circulation (MOC) over the last deglaciation. In this study, we present a compilation of existing and new sedimentary 231Pa/230Th records from North Atlantic cores between 1710 and 4550 m water depth. Comparing sedimentary 231Pa/230Th from different depths provides new insights into the evolution of the geometry and rate of deep water formation in the North Atlantic during the last 20,000 years. The 231Pa/230Th ratio measured in upper Holocene sediments indicates slow water renewal above ∼2500 m and rapid flushing below, consistent with our understanding of modern circulation. In contrast, during the Last Glacial Maximum (LGM), Glacial North Atlantic Intermediate Water (GNAIW) drove a rapid overturning circulation to a depth of at least ∼3000 m depth. Below ∼4000 m, water renewal was much slower than today. At the onset of Heinrich event 1, transport by the overturning circulation declined at all depths. GNAIW shoaled above 3000 m and significantly weakened but did not totally shut down. During the Bølling‐Allerød (BA) that followed, water renewal rates further decreased above 2000 m but increased below. Our results suggest for the first time that ocean circulation during that period was quite distinct from the modern circulation mode, with a comparatively higher renewal rate above 3000 m and a lower renewal rate below in a pattern similar to the LGM but less accentuated. MOC during the Younger Dryas appears very similar to BA down to 2000 m and slightly slower below.
Curation of NISEED, an integrative framework for the digital representation of embryonic development
Authors: Dauga Delphine , Tassy Olivier , Daian Fabrice , Sobral Daniel , Lemaire Patrick
Published: April 2009

NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its neighbors, or at the level of the whole embryo by representing its anatomy and morphogenesis at successive developmental stages. The system provides also tool and standard to enter, annotate, curate and manage data. All results can be accessed through the ANISEED website at "http://aniseed-ibdm.univ-mrs.fr":http://aniseed-ibdm.univ-mrs.fr
Study of planktonic morphotype of the Abderaz Formation at type section, Iran
Authors: Shafiee Ardestani Meysam
Published: May 2009

Abderaz Formation at its type section with an age of Turonian-Early Campanian and a thickness of 300 m contains light grey shale and marl. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation.
Androgen Receptor and Vasopressin Receptor (AVPR1a) Genetic Polymorphisms are not associated with Marital Status or Fertility among Ariaal Men of Northern Kenya
Authors: Gray Peter , Eisenberg Dan , Campbell Benjamin
Published: May 2009

A growing body of scholarship implicates testosterone and vasopressin in male reproductive behavior, including in humans. Since hormones exert their effects through their respective receptors, an open question has been whether genetic polymorphisms in the androgen receptor and vasopressin 1a receptor (AVPR1a) impact human male social behavior. Here, we sought to test for associations between polymorphisms in the coding region of the androgen receptor and promoter region of AVPR1a in relation to marital status and fertility among pastoralist Ariaal men of northern Kenya. None of the three polymorphisms were related to marital status (single, monogamously married, polygynously married) or fertility (number of current living children). We discuss these null findings in light of existing data.
Health Literacy and the Role of the Speech-Language Pathologist
Authors: Hester Eva Jackson , Stevens-Ratchford Regena
Published: May 2009

Purpose

This article reviews concepts of health literacy and discusses the role of speech-language pathologists in improving the health literacy of individuals with and without communication disorders.

Method

A literature review was completed of health literacy definitions, concepts, and health literacy assessment and intervention studies with various populations. A literature review was also conducted regarding health literacy or related studies in the field of speech-language pathology.

Conclusion

There is a paucity of information available on health literacy within the field of speech-language pathology. Suggestions are offered regarding increasing health literacy research and intervention by speech-language pathologists.
X-ray diffraction of electrodeposited nanocrystalline nickel under high pressure
Authors: Grant C. D. , Crowhurst J. C. , Arsenlis T. , Bringa E. M. , Wang Y. M. , Hawreliak J. A. , Pauzauskie P. J. , Clark S. M.
Published: April 2009

We studied the compressibility of monolithic fully dense electrodeposited nanocrystalline Ni (∼29 nm grain size) under both quasihydrostatic and nonhydrostatic conditions up to a nominal pressure of 50 GPa using angle-dispersive x-ray diffraction. We obtained an equation of state consistently and unambiguously from each measured reflection. The apparent bulk modulus measured under nonhydrostatic conditions is larger than that of the corresponding coarse-grained material under either type of compression, but is nearly the same when measured under quasihydrostatic conditions. These results may be consistent with a strength, but not necessarily a bulk modulus, that is enhanced in the nanomaterial relative to its coarse-grained counterparts.
Ultrasound screening for fetal structural abnormalities performed by trained midwives in the second trimester in a low‐risk population – an appraisal
Authors: CHEN MIN , LEUNG TAK YEUNG , SAHOTA DALJIT SINGH , FUNG TAK YUEN , CHAN LIN WAI , LAW LAI WA , CHAU MO CHING , LAO TZU‐HSI TERENCE , LAU TZE KIN
Published: May 2009

Objective. To determine the performance of trained midwives in second trimester ultrasound screening for fetal structural abnormalities in a low‐risk population. Design. Retrospective study. Setting. University Department of Obstetrics and Gynecology. Population. About 13,882 women with singleton pregnancies. Methods. The findings of routine second trimester anomaly scan performed by midwives were reviewed. Reasons for referral to maternal fetal medicine (MFM) specialists for further assessment were analyzed. Main outcome measures. The detection, false positive and false alarm rates for fetal anomalies. Results. One hundred and eighty‐nine pregnancies with unknown outcome were excluded from the final analysis. Overall, 617 (4.51%) women were referred to MFM specialists for further assessment, of which 470 (70.2%) were for soft markers alone and 147 (23.8%) for suspected fetal structural abnormalities. In these 13,693 fetuses with known outcome, malformed fetuses were present in 185, a prevalence of 1.35%. Of these, 115 were detected during the second trimester scan and two were detected in the third trimester. The remaining 68 malformed fetuses, most of which had minor anomalies, were identified after birth. The detection rate for a malformed fetus in second trimester scan was 62.2% (115/185) (95% CI 55.2–69.2). There were four cases of false positives and 33 cases of false alarm. Conclusions. Experienced midwives with proper training can detect the majority of major structural abnormalities. Continuous audit and quality control plays a significant role in optimizing the fetal structural examination.
‘Fitting in’ or ‘standing out’: Working‐class students in UK higher education
Authors: Reay Diane , Crozier Gill , Clayton John
Published: April 2009

Drawing on case studies of 27 working‐class students across four UK higher education institutions, this article attempts to develop a multilayered, sociological understanding of student identities that draws together social and academic aspects. Working with a concept of student identity that combines the more specific notion of learner identity with more general understandings of how students are positioned in relation to their discipline, their peer group and the wider university, the article examines the influence of widely differing academic places and spaces on student identities. Differences between institutions are conceptualised in terms of institutional habitus, and the article explores how the four different institutional habituses result in a range of experiences of fitting in and standing out in higher education. For some this involves combining a sense of belonging in both middle‐class higher education and working‐class homes, while others only partially absorb a sense of themselves as students.
Insulin Inhibits Low Oxygen‐Induced ATP Release from Human Erythrocytes: Implication for Vascular Control
Authors: HANSON MADELYN S. , ELLSWORTH MARY L. , ACHILLEUS DAVID , STEPHENSON ALAN H. , BOWLES ELIZABETH A. , SRIDHARAN MEERA , ADDERLEY SHAQURIA , SPRAGUE RANDY S.
Published: May 2009

Objective: ATP released from human erythrocytes in response to reduced oxygen tension (pO2) participates in the matching of oxygen (O2) supply with need in skeletal muscle by stimulating increases in blood flow to areas with increased O2 demand. Here, we investigated the hypothesis that hyperinsulinemia inhibits ATP release from erythrocytes and impairs their ability to stimulate dilation of isolated arterioles exposed to decreased extraluminal pO2. Materials andMethods: Erythrocyte ATP release was stimulated pharmacologically (mastoparan 7) and physiologically (reduced pO2) in the absence or presence of insulin. We also examined the ability of isolated skeletal muscle arterioles perfused with buffer containing erythrocytes treated with insulin or its vehicle (saline) to dilate in response to decreased extraluminal pO2. Results: Insulin significantly attenuated mastoparan 7– and reduced pO2–induced ATP release. In vessels perfused with untreated erythrocytes, low extraluminal pO2 resulted in an increase in vessel diameter. In contrast, when erythrocytes were treated with insulin, no vasodilation occurred. Conclusions: These studies demonstrate that insulin inhibits ATP release from erythrocytes in response to reduced pO2 and impairs their ability to stimulate dilation of skeletal muscle arterioles. These results suggest that hyperinsulinemia could hinder the matching of O2 supply with need in skeletal muscle.
On Control of Reaching Movements for Musculo‐Skeletal Redundant Arm Model
Authors: Tahara Kenji , Arimoto Suguru , Sekimoto Masahiro , Luo Zhi-Wei
Published: May 2009

This paper focuses on a dynamic sensory‐motor control mechanism of reaching movements for a musculo‐skeletal redundant arm model. The formulation of a musculo‐skeletal redundant arm system, which takes into account non‐linear muscle properties obtained by some physiological understandings, is introduced and numerical simulations are perfomed. The non‐linear properties of muscle dynamics make it possible to modulate the viscosity of the joints, and the end point of the arm converges to the desired point with a simple task‐space feedback when adequate internal forces are chosen, regardless of the redundancy of the joint. Numerical simulations were performed and the effectiveness of our control scheme is discussed through these results. The results suggest that the reaching movements can be achieved using only a simple task‐space feedback scheme together with the internal force effect that comes from non‐linear properties of skeletal muscles without any complex mathematical computation such as an inverse dynamics or optimal trajectory derivation. In addition, the dynamic damping ellipsoid for evaluating how the internal forces can be determined is introduced. The task‐space feedback is extended to the ‘virtual spring‐damper hypothesis’ based on the research by Arimoto et al. (2006) to reduce the muscle output forces and heterogeneity of convergence depending on the initial state and desired position. The research suggests a new direction for studies of brain‐motor control mechanism of human movements.
Progress and prospects of ion-driven fast ignition
Authors: Fernández Juan C. , Honrubia J.J. , Albright Brian J. , Flippo Kirk A. , Gautier D. Cort , Hegelich Björn M. , Schmitt Mark J. , Temporal M. , Yin Lin
Published: May 2009

Fusion fast ignition (FI) initiated by laser-driven ion beams is a promising concept examined in this paper. FI based on a beam of quasi-monoenergetic ions (protons or heavier ions) has the advantage of a more localized energy deposition, which minimizes the required total beam energy, bringing it close to the ≈10 kJ minimum required for fuel densities ∼500 g cm−3. High-current, laser-driven ion beams are most promising for this purpose. Because they are born neutralized in picosecond timescales, these beams may deliver the power density required to ignite the compressed DT fuel, ∼10 kJ/10 ps into a spot 20 µm in diameter. Our modelling of ion-based FI include high fusion gain targets and a proof of principle experiment. That modelling indicates the concept is feasible, and provides confirmation of our understanding of the operative physics, a firmer foundation for the requirements, and a better understanding of the optimization trade space. An important benefit of the scheme is that such a high-energy, quasi-monoenergetic ignitor beam could be generated far from the capsule (⩾1 cm away), eliminating the need for a reentrant cone in the capsule to protect the ion-generation laser target, a tremendous practical benefit. This paper summarizes the ion-based FI concept, the integrated ion-driven FI modelling, the requirements on the ignitor beam derived from that modelling, and the progress in developing a suitable laser-driven ignitor ion beam.
Temporal changes in maturation, mean length-at-age, and condition of spring-spawning Atlantic herring (Clupea harengus) in Newfoundland waters
Authors: Wheeler J. P. , Purchase C. F. , Macdonald P. D. M. , Fill R. , Jacks L. , Wang H. , Ye C.
Published: May 2009

Wheeler, J. P., Purchase, C. F., Macdonald, P. D. M., Fill, R., Jacks, L., Wang, H., and Ye, C. 2009. Temporal changes in maturation, mean length-at-age, and condition of spring-spawning Atlantic herring (Clupea harengus) in Newfoundland waters. – ICES Journal of Marine Science, 66: 1800–1807. We investigated temporal trends in some life-history traits of Atlantic herring. Population size of Newfoundland herring stock complexes declined precipitously through the 1970s. Maturation age and size also decreased substantially, but not until the late 1980s. Although significant effects were found for region and gear type, these were only minor compared with the general trend. No effects were found for sex. Changes in maturation age and size can represent an evolutionary response to fishery-induced selection, or phenotypic plasticity as a result of a compensatory response to stock declines, or a response to other changes in the environment. Length-at-age and body condition decreased concurrently with changes in maturation, suggesting that declines in maturation age and size were not a compensatory response to reduced stock sizes. This supports the hypothesis of evolutionary changes in maturation. However, increases observed in the most recent year classes, and concurrent changes in other species, suggest that changes in the environment may have also affected age- and size-at-maturation.
Fine-scaled human genetic structure revealed by SNP microarrays
Authors: Xing Jinchuan , Watkins W. Scott , Witherspoon David J. , Zhang Yuhua , Guthery Stephen L. , Thara Rangaswamy , Mowry Bryan J. , Bulayeva Kazima , Weiss Robert B. , Jorde Lynn B.
Published: May 2009

We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.
Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes
Authors: Norman Paul J. , Abi-Rached Laurent , Gendzekhadze Ketevan , Hammond John A. , Moesta Achim K. , Sharma Deepti , Graef Thorsten , McQueen Karina L. , Guethlein Lisbeth A. , Carrington Christine V.F. , Chandanayingyong Dasdayanee , Chang Yih-Hsin , Crespí Catalina , Saruhan-Direskeneli Güher , Hameed Kamran , Kamkamidze Giorgi , Koram Kwadwo A. , Layrisse Zulay , Matamoros Nuria , Milà Joan , Park Myoung Hee , Pitchappan Ramasamy M. , Ramdath D. Dan , Shiau Ming-Yuh , Stephens Henry A.F. , Struik Siske , Tyan Dolly , Verity David H. , Vaughan Robert W. , Davis Ronald W. , Fraser Patricia A. , Riley Eleanor M. , Ronaghi Mostafa , Parham Peter
Published: May 2009

Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here isKIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the3DL1and3DL2genes produced a deletedKIRhaplotype in which the telomeric “half” was reduced to a single fusion gene with functional properties distinct from its3DL1and3DL2parents. Conversely, in Eurasian populations, duplication of theKIR3DL1/S1locus by unequal crossing over has enabled individuals to carry and express alleles of all threeKIR3DL1/S1lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving humanKIRgene family.
Recovering genome rearrangements in the mammalian phylogeny
Authors: Zhao Hao , Bourque Guillaume
Published: May 2009

The analysis of genome rearrangements provides a global view on the evolution of a set of related species. We present a new algorithm called EMRAE (efficient method to recover ancestral events) to reliably predict a wide-range of rearrangement events in the ancestry of a group of species. Using simulated data sets, we show that EMRAE achieves comparable sensitivity but significantly higher specificity when predicting evolutionary events relative to other tools to study genome rearrangements. We apply our approach to the synteny blocks of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog) and predict 1109 rearrangement events, including 831 inversions, 15 translocations, 237 transpositions, and 26 fusions/fissions. Studying the sequence features at the breakpoints of the primate rearrangement events, we demonstrate that they are not only enriched in segmental duplications (SDs), but that the enrichment of matching pairs of SDs is even stronger within the pairs of breakpoints associated with recovered events. We also show that pairs of L1 repeats are frequently associated with ancestral inversions across all studied lineages. Together, this substantiates the model that regions of high sequence identity have been associated with rearrangement events throughout the mammalian phylogeny.
Constructing genomic maps of positive selection in humans: Where do we go from here?
Authors: Akey Joshua M.
Published: May 2009

Identifying targets of positive selection in humans has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of natural selection. To date, 21 genome-wide scans for recent or ongoing positive selection have been performed in humans. A key challenge is to begin synthesizing these newly constructed maps of positive selection into a coherent narrative of human evolutionary history and derive a deeper mechanistic understanding of how natural populations evolve. Here, I chronicle the recent history of the burgeoning field of human population genomics, critically assess genome-wide scans for positive selection in humans, identify important gaps in knowledge, and discuss both short- and long-term strategies for traversing the path from the low-resolution, incomplete, and error-prone maps of selection today to the ultimate goal of a detailed molecular, mechanistic, phenotypic, and population genetics characterization of adaptive alleles.
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila
Authors: Findlay Geoffrey D. , MacCoss Michael J. , Swanson Willie J.
Published: May 2009

As genomic sequences become easier to acquire, shotgun proteomics will play an increasingly important role in genome annotation. With proteomics, researchers can confirm and revise existing genome annotations and discover completely new genes. Proteomic-based de novo gene discovery should be especially useful for sets of genes with characteristics that make them difficult to predict with gene-finding algorithms. Here, we report the proteomic discovery of 19 previously unannotated genes encoding seminal fluid proteins (Sfps) that are transferred from males to females during mating in Drosophila. Using bioinformatics, we detected putative orthologs of these genes, as well as 19 others detected by the same method in a previous study, across several related species. Gene expression analysis revealed that nearly all predicted orthologs are transcribed and that most are expressed in a male-specific or male-biased manner. We suggest several reasons why these genes escaped computational prediction. Like annotated Sfps, many of these new proteins show a pattern of adaptive evolution, consistent with their potential role in influencing male sperm competitive ability. However, in contrast to annotated Sfps, these new genes are shorter, have a higher rate of nonsynonymous substitution, and have a markedly lower GC content in coding regions. Our data demonstrate the utility of applying proteomic gene discovery methods to a specific biological process and provide a more complete picture of the molecules that are critical to reproductive success in Drosophila.
Computational Docking of Biomolecular Complexes with AutoDock
Authors: Goodsell David S.
Published: May 2009

INTRODUCTION

Computer prediction of the interaction between enzymes and small molecules has now advanced to the point that it allows accurate prediction of bound conformations and binding constants. For instance, the program AutoDock allows consistent computational docking of flexible ligands with about a dozen torsional degrees of freedom, and the empirical free-energy force field provides predicted energies that are accurate to within ~2 kcal/mol, or an ~30-fold difference in binding constants. Thus, these methods can easily separate compounds with micromolar and nanomolar binding constants from those with millimolar binding constants, and can often rank molecules with finer differences in affinity. Computational docking methods can be used to screen a variety of possible compounds, searching for new compounds with specific binding properties or testing a range of modifications of an existing compound. The approach has been successful in numerous cases, most notably, the discovery of human immunodeficiency virus (HIV) protease inhibitors. This protocol presents a detailed outline and advice for use of AutoDock and its graphical interface, AutoDock Tools, to analyze biomolecular complexes using computational docking. The first step is to prepare the coordinate files for the docking molecule and the target molecule. The second step is the calculation of the affinity grid for the target molecule. In the third step, the docking molecule is docked with the affinity grid, and, finally, the results are analyzed.
Surgical Manipulations on Pupal Wings from the African Butterfly Bicyclus anynana: Damage and Cauteries
Authors: Brakefield Paul M. , Beldade Patrícia , Zwaan Bas J.
Published: May 2009

INTRODUCTION

This protocol describes cautery experiments with young pupal wings of the African butterfly Bicyclus anynana to examine the potential role of groups of cells in wing pattern determination. Experiments can be performed on either the left or right wing, leaving the other wing as a control. The pupal wing case overlies a stack of four sheets of epithelial cells that will form, in turn, the dorsal and ventral surfaces of the forewing and then the respective surfaces of the hindwing. The dorsal surface of the forewing is immediately underneath the cuticle. The trachea or wing veins of the forewing are visible through the pupal cuticle under a binocular microscope, providing landmarks. Raised “bumps” or irregularities on the pupal cuticle indicate where the eyespot organizers (or foci) are present on the underlying forewing. The wild-type pattern of the dorsal forewing consists of a small anterior eyespot and a large posterior eyespot; each eyespot has a central white pupil, a black inner ring, and an outer gold ring. Experiments that involve a short insertion of sharpened needles through the pupal cuticle can explore the effects of damage to groups of cells at different times from shortly after pupation until pattern determination has occurred (~24 h after pupation). This type of experiment originally helped to characterize the eyespot organizers because early focal damage to the location of these cells can result in shrinkage or complete elimination of the corresponding eyespot in the adult wing (relative to the control wing).
Fixation and Dissection of Embryos from the African Butterfly Bicyclus anynana
Authors: Brakefield Paul M. , Beldade Patrícia , Zwaan Bas J.
Published: May 2009

INTRODUCTION

This protocol describes a procedure for the fixation and dissection of embryos from the African butterfly Bicyclus anynana. Such embryos can be used subsequently for in situ hybridization experiments or for immunohistochemistry analysis.
In Situ Hybridization of Embryos and Larval and Pupal Wings from the African Butterfly Bicyclus anynana
Authors: Brakefield Paul M. , Beldade Patrícia , Zwaan Bas J.
Published: May 2009

INTRODUCTION

The modified in situ hybridization protocol described here can be used to localize RNA transcripts in developing tissues of the African butterfly Bicyclus anynana, including larval and pupal wings and embryos.
Extraction and Gas Chromatography Analysis of Adult Pheromones from the African Butterfly Bicyclus anynana
Authors: Brakefield Paul M. , Beldade Patrícia , Zwaan Bas J.
Published: May 2009

INTRODUCTION

Pheromones are used for communication among individuals of the same species, including attracting mates. A blend of chemical components is recognized as a pheromone if it elicits a behavioral or physiological response. Gas chromatography (GC) helps to separate complex mixtures of chemicals extracted from a target tissue. When the extract is associated with an internal standard, GC can be used to quantify the amounts of the chemical components present on a target tissue. This protocol describes the preparation of pheromone extracts from wings of the African butterfly Bicyclus anynana and the subsequent use of these extracts in GC analysis.
Injection of Chemicals into Pupae of the African Butterfly Bicyclus anynana
Authors: Brakefield Paul M. , Beldade Patrícia , Zwaan Bas J.
Published: May 2009

INTRODUCTION

This protocol describes a procedure for the injection of chemicals into pupae of the African butterfly Bicyclus anynana. A number of target traits can be monitored to determine the effect of a particular chemical on the pupae.
Construction of Fusion Proteins for Transductional Targeting: Figure 1.
Authors: Kawakami Yosuke , Curiel David T.
Published: May 2009

INTRODUCTION

Therapeutic gene transfer strategies aim to maximize gene transfer and expression in target cells. However, gene delivery systems often fail to preferentially transduce target cells in mixed cell populations. In addition, limitations in vector specificity can lead to transduction of nontarget cells, resulting in untoward toxicity, even with compartmental dosing. Thus, vector optimization is critical for the development of efficient genetic experiments. The life cycle and biology of adenovirus (Ad) infection and transgene expression in cells have been thoroughly characterized. Ad infection is initiated by recognition of the native Ad5 receptor, coxsackievirus-adenovirus receptor (CAR), on target cells by the carboxy-terminal portion (i.e., knob) of the fiber protein. The development of genetically modified Ad vectors with transductional specificity for a single cell type requires “retargeting:” the ablation of endogenous tropism and the introduction of novel tropism determinants for target cells. One strategy for accomplishing such retargeting does so indirectly, by using bifunctional adapter molecules. One element of the bispecific adapter binds to the Ad fiber knob, blocking its interaction with CAR and, thus, its native tropism. The second component of the adapter introduces specificity for the target cells and is chemically or genetically conjugated to the knob-binding portion. Recombinant fusion proteins offer a number of technological advantages over chemical conjugates, including simplified production and purification. In this protocol, a recombinant fusion protein is generated that ablates the vector’s native tropism by blocking the CAR receptor and retargets the vector to cells expressing epidermal growth factor (EGF).