bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns of polychaete communities in relation to environmental perturbations in a subtropical wetland of Hong Kong
Authors: Shen Ping-Ping , Zhou Hong , Gu Ji-Dong
Published: July 2010

Benthic polychaetes in the largest intertidal mudflat of Hong Kong were analysed for potentially stressed environmental conditions from pollution. Over a two-year period, a total of 14 species were recorded with the species diversity (H′(log2)) ranged from 0.54 to 2.4. The community was dominated by two large polychaetes (Neanthes glandicincta and Potamilla acuminata) and a number of small pollution tolerant species (Tharyx, Capitella capitata and Prionospio cirrifera). It was also characterized by both temporal and spatial variations in terms of abundance and species composition with the lowest species number observed at onshore Station B in August and the highest at offshore Station D in February. Two distinct polychaete communities were formed along the intertidal towards subtidal mudflat, particularly the assemblage at onshore Station B showing a significant difference from those at the other three stations (P < 0.05, N = 32). Results of the abundance–biomass comparison (ABC) indicated a typical impacted community at the whole study area, especially at Station B which was close to the Shenzhen River mouth and mangrove forest. The total organic carbon had a significant positive effect on the abundance of Capitella capitata (P = 0.037, N = 8) while sedimentary compositions were statistically related to the abundance of Potamilla acuminata, Tharyx and total abundance of polychaetes (P < 0.05, N = 8). In conclusion, both the polluted Shenzhen River and nearby mangrove may be responsible for the decline in species richness and diversity as well as changes in community structure. Polychaetes can be used as the appropriate indicators in habitat ecological condition assessment instead of the whole benthic community.
Abundance, size and habitat relation of reef fish on biogenic structures (structure-forming invertebrates) at Anacapa Island, southern California
Authors: Zalmon Ilana Rosental , McCrea Merit , Love Milton Stevens
Published: July 2010

A biogenic structure ecosystem of extensive worm tubes of Chaetopterus sp. harbouring different fish species was investigated at Anacapa Island, southern California to determine the numerical abundance, species composition, body size, and seasonality of the ichthyofauna associated, and their relation with the worm patch size. Bimonthly, a 30-m swimming transect and a quadrat-based survey estimated the length of each fish, the type of habitat it occupied, and the worm tube patch size-class. Larger worm mats harboured higher densities of fish, mainly the dominants Rhinogobiops nicholsii and Chaenopsis alepidota, which live inside the worm tube patches. Fish population density varied between the ‘inside’ and ‘edge’ of Chaetopterus beds as smaller and younger individuals were hindered from reaching the middle of the patch by larger, older and territorial individuals. The prevalence of positive and significant correlations between the abundance of smaller individuals of R. nicholsii and specific habitat features (e.g. edge) suggests that the abundance and distribution of juveniles might be habitat-dependent besides intraspecific competition between older and younger individuals. There was a decreasing density of R. nicholsii at greater than 20 cm away from worm tubes and there were no individuals beyond 6 m away from structure. Chaenopsis alepidota was not recorded when the patch size was less than 50% tube coverage. Our results revealed that complex habitat structure had a positive influence on the abundance of juvenile and adult of C. alepidota and R. nicholsii, and suggest that these structured areas are preferentially utilized, which contributes to its patchy distribution pattern. The presence of biological structures in low-relief sedimentary habitats can have critical functional significance even for reef fish. These important habitat features may need to be identified and protected.
Interactions between immunity and metabolism – contributions from the metabolic profiling of parasite-rodent models
Authors: SARIC J.
Published: July 2010

A combined interdisciplinary research strategy is even more crucial in immunology than in many other biological sciences in order to comprehend the closely linked interactions between cell proliferation, molecular signalling and gene rearrangements. Because of the multi-dimensional nature of the immune system, an abundance of different experimental approaches has developed, with a main focus on cellular and molecular mechanisms. The role of metabolism in immunity has been underexplored so far, and yet researchers have made important contributions in describing associations of immune processes and metabolic pathways, such as the central role of thel-arginine pathway in macrophage activation or the immune regulatory functions of the nucleotides. Furthermore, metabolite supplement studies, including nutritional administration and labelled substrates, have opened up new means of manipulating immune mechanisms. Metabolic profiling has introduced a reproducible platform for systemic assessment of changes at the small-molecule level within a host organism, and specific metabolic fingerprints of several parasitic infections have been characterized by1H NMR spectroscopy. The application of multivariate statistical methods to spectral data has facilitated recovery of biomarkers, such as increased acute phase protein signals, and enabled direct correlation to the relative cytokine levels, which encourages further application of metabolic profiling to explore immune regulatory systems.
Britannia 40 Years: Roman Society 100 Years
Authors: Frere S.S. , Goodburn R.
Published: July 2010

Britannia. The birth and growth of the Roman Society’s second journal: a centennial assessment.
Legionary Tile Production in Britain
Authors: Warry Peter
Published: July 2010

There are over two thousand legionary stamped tiles incorporating some two hundred different dies now admirably collated and listed inRoman Inscriptions of Britain. Dates have been tentatively suggested for a minority of these dies, but some of these are inconsistent with the other evidence. Inter alia, by using dating derived from the different forms of tegulae on which these stamps have been impressed, revised dating is proposed. Linking these dates with the distribution of the stamped tiles sheds new light on legionary practices and movements, particularly on Hadrian’s Wall and in post-Antonine Scotland, as well as the relationship between the legions and the auxiliary units. The multiplicity of different dies could be explained by each cohort having its own stamp and stamping every one of the tiles they produced, a practice that all the British legions seem to have followed. The discovery oflegio XXstamped tiles referring to Viducius at a rural tile-works in Merseyside confirms him as a legionary contractor; close examination of tile sizes shows that contractors appear to have played a significant part in the production for at least two of the legions.
‘Horrible, Speculative, Nasty, Dangerous’: Assessing the Value of Roman Iron
Authors: Bray Lee
Published: July 2010

The economic aspects of metallurgy in the distant past have been relatively little studied, largely owing to the absence of detailed records for periods preceding medieval times. This paper takes advantage of a rare survival, an account from the Vindolanda tablets in which a price for iron is recorded, to explore some of the economic characteristics of the metal during the first and second centuriesa.d.in Britain. The inherent difficulties in employing evidence of this kind are examined before looking at the price information from the rest of the Vindolanda tablets to assess the value of iron relative to other commodities at the fort. The value of the metal is then examined compared with that of labour, thus illuminating the potential economic opportunities that became available to iron producers following the establishment of Roman rule in Britain.
An Inscription from Bavai and the Fifth-Century Christian Epigraphy of Britain
Authors: Knight Jeremy K.
Published: July 2010

The consular dated memorial of a military accountant (scrinarius) ofa.d.404 with a chi-rho monogram from Bavai (France, Nord), previously thought to be a forgery, is reconsidered. Geographically close to Britain and well-dated, it is relevant to the origins of post-Roman insular epigraphy and to the possibility of recognising specifically Christian tombstones in Roman Britain. The insular series derives from a late antique tradition introduced to Britain via the Christian Church at an uncertain date. There is little sign of continuity with claimed Romano-British Christian tombstones, but an early phase of the insular series can be recognised. Literacy and perhaps the ‘epigraphic habit’ survived in other media.
Problem-solving abilities and frontal lobe cortical thickness in healthy aging and mild cognitive impairment
Authors: SÁNCHEZ-BENAVIDES G. , GÓMEZ-ANSÓN B. , QUINTANA M. , VIVES Y. , MANERO R.M. , SAINZ A. , BLESA R. , MOLINUEVO J.L. , PEÑA-CASANOVA J.
Published: July 2010

Mild cognitive impairment (MCI) is considered a transitional state between normal aging and Alzheimer disease. Most MCI subjects present disturbances in multiple neuropsychological domains, including executive function. This study aimed at exploring frontal lobe cortical thinning in MCI and healthy controls, and its relationship with problem-solving abilities. Twenty-three MCI patients and 30 elderly controls underwent MRI and neuropsychological assessment. Cortical thickness was measured by means of FreeSurfer. Problem-solving was assessed by means of the Tower of London (TOL) task. MCI showed a global thinning of the cortex. With regard to specific regions of interest, a thinning in the left frontal lobe and the bilateral posterior cingulate gyri was found. Partial correlations, after controlling for age, education, Mini-Mental Status Examination, and non-frontal mean thickness revealed negative significant correlations between frontal lobe thickness and executive outcomes in the control group. This counterintuitive relationship was not observed in the MCI group, suggesting that the frontal cortical atrophy observed in MCI entails a specific pathology-related relationship with high-level executive outcomes that is qualitatively different from that observed in healthy aging. (JINS, 2010, 16, 836–845.)
Aberration Correction and Electron Holography
Authors: Lichte Hannes , Linck Martin , Geiger Dorin , Lehmann Michael
Published: July 2010

Electron holography has been shown to allow a posteriori aberration correction. Therefore, an aberration corrector in the transmission electron microscope does not seem to be needed with electron holography to achieve atomic lateral resolution. However, to reach a signal resolution sufficient for detecting single light atoms and very small interatomic fields, the aberration corrector has turned out to be very helpful. The basic reason is the optimized use of the limited number of “coherent” electrons that are provided by the electron source, as described by the brightness. Finally, quantitative interpretation of atomic structures benefits from the holographic facilities of fine-tuning of the aberration coefficients a posteriori and from evaluating both amplitude and phase.
Evidence that core histone H3 is targeted to the mitochondria in Brassica oleracea
Authors: Zanin Mary Katherine B. , Donohue Jon M. , Everitt Bryan A.
Published: July 2010

The core histone proteins H2A, H2B, H3 (histone H3) and H4 are known to form nucleosomes with nuclear DNA, but are historically considered to be absent from mitochondria. We suggest that H3 is a dual‐targeted protein, found in mitochondria as well as N (nuclei). WoLF PSORT and MitoProt analyses of H3 sequences revealed mitochondrial targeting signals, and immunohistochemistry indicated mitochondrial distribution. Western blots of Brassica oleracea cv. Botrytis (cauliflower) mitochondrial extracts were positive for H3, when the primary antibody was against the conserved C‐terminus. MS/MS (tandem mass spectrometry) analyses confirmed the Western blot data. Interestingly, Western blots of the same mitochondrial extracts were almost completely negative for H3 when the primary antibodies were highly specific for the N‐terminal tail region of H3, suggesting that these antibodies are blocked by a modification of the tail of the H3 that occurs predominantly in the mitochondria, but not in the nucleus. Modifications of the tail of core H3 are known to help control nuclear genes. Future studies of the possible functions of mitochondrial H3 could lead to a greater understanding of the ability of a cell to synchronize nuclear and mitochondrial gene expression.
Islam and democracy
Authors: Howeidy Fahmy
Published: July 2010

This paper reviews how the civilizational discourse of Islam differs from that of democracy but doesn’t necessarily mean that it contradicts it. Knowing that this juxtaposition promotes diversity and distinction, this paper elucidates the factors of ambiguity that surround this religion and system in order to uncover the real dimension of their distinction. The paper is organized as follows: first, it presents seven characteristics of the Islamic state. Next, it discusses the importance of consultation (al-shūrā) and the necessity of questioning the rulers in Islam. Third, the article answers the question “Where does democracy correspond to Islam and where does it differ?”. Several prominent opinions are examined in the fourth part, before displaying the main positions from the 1980s, vis-à-vis democracy, in part five. Part six exhibits the fatwas of al-Qaradawi. At the end of the article, the paper emphasizes the approaches that can be taken towards Islamic ruling (sharīꜥah).
Creatively re-imagining a new Sudanese nation: towards achieving conditional unity
Authors: Deng Francis M. , El-Affendi Abdelwahab
Published: July 2010

Sudan is facing the most crucial challenge of its history with the referendum on unity in the South planned for January 2011. In this paper, the two authors attempt to assess the nature of the challenge, and explore possible scenarios and options for dealing with the decision and its aftermath. The central argument is that there is a need for a radical restructuring of the Sudanese state to enable and promote a sense of belonging and nationhood which could safeguard unity and avoid a recurrence of conflict. Taking its cue from the emerging consensus among the main actors to safeguard unity within a loose federal/confederal framework, the paper argues that devising a flexible and inclusive system of governance capable of accommodating Sudan’s diversity is the key to meeting this challenge. In the short term, there is a need to adopt a more realistic and pragmatic approach based on accommodating the interests of key political players. The international community also needs to be more proactive and engaged that at present.
PI3 kinase signalling blocks Foxp3 expression by sequestering Foxo factors
Authors: Merkenschlager Matthias , von Boehmer Harald
Published: July 2010

Expression of the regulatory T (T reg) cell–associated transcription factor Foxp3 can be induced by signals from the T cell receptor (TCR), interleukin-2 (IL-2), and transforming growth factor (TGF)-β. These signals are integrated by a network involving phosphatidylinositol 3 kinase (PI3K), protein kinase B (PKB; here referred to as Akt), and the mammalian target of rapamycin (mTOR). New studies show that the Foxo proteins Foxo1 and Foxo3a, which are inactivated by Akt, drive Foxp3 expression. These studies therefore explain the negative regulation of Foxp3 by PI3K signaling, and add Foxo proteins to the growing list of nuclear factors capable of modulating Foxp3 expression.
Quantum analogue computing
Authors: Kendon Vivien M. , Nemoto Kae , Munro William J.
Published: July 2010

We briefly review what a quantum computer is, what it promises to do for us and why it is so hard to build one. Among the first applications anticipated to bear fruit is the quantum simulation of quantum systems. While most quantum computation is an extension of classical digital computation, quantum simulation differs fundamentally in how the data are encoded in the quantum computer. To perform a quantum simulation, the Hilbert space of the system to be simulated is mapped directly onto the Hilbert space of the (logical) qubits in the quantum computer. This type of direct correspondence is how data are encoded in a classical analogue computer. There is no binary encoding, and increasing precision becomes exponentially costly: an extra bit of precision doubles the size of the computer. This has important consequences for both the precision and error-correction requirements of quantum simulation, and significant open questions remain about its practicality. It also means that the quantum version of analogue computers, continuous-variable quantum computers, becomes an equally efficient architecture for quantum simulation. Lessons from past use of classical analogue computers can help us to build better quantum simulators in future.
Strongly interacting dynamics beyond the standard model on a space–time lattice
Authors: Lucini Biagio
Published: July 2010

Strong theoretical arguments suggest that the Higgs sector of the standard model of electroweak interactions is an effective low-energy theory, with a more fundamental theory expected to emerge at an energy scale of the order of a teraelectronvolt. One possibility is that the more fundamental theory is strongly interacting and the Higgs sector is given by the low-energy dynamics of the underlying theory. I review recent works aimed at determining observable quantities by numerical simulations of strongly interacting theories proposed in the literature to explain the electroweak symmetry-breaking mechanism. These investigations are based on Monte Carlo simulations of the theory formulated on a space–time lattice. I focus on the so-called minimal walking technicolour scenario, an SU(2) gauge theory with two flavours of fermions in the adjoint representation. The emerging picture is that this theory has an infrared fixed point that dominates the large-distance physics. I shall discuss the first numerical determinations of quantities of phenomenological interest for this theory and analyse future directions of quantitative studies of strongly interacting theories beyond the standard model with lattice techniques. In particular, I report on a finite size scaling determination of the chiral condensate anomalous dimension
γ
, for which 0.05≤
γ
≤0.25.
Automatic lexical classification: bridging research and practice
Authors: Korhonen Anna
Published: July 2010

Natural language processing (NLP)—the automatic analysis, understanding and generation of human language by computers—is vitally dependent on accurate knowledge about
words
. Because words change their behaviour between text types, domains and sub-languages, a fully accurate static lexical resource (e.g. a dictionary, word classification) is unattainable. Researchers are now developing techniques that could be used to automatically acquire or update lexical resources from textual data. If successful, the automatic approach could considerably enhance the accuracy and portability of language technologies, such as machine translation, text mining and summarization. This paper reviews the recent and on-going research in automatic lexical acquisition. Focusing on lexical classification, it discusses the many challenges that still need to be met before the approach can benefit NLP on a large scale.
Triggered infrared spectroscopy for investigating metalloprotein chemistry
Authors: Vincent Kylie A.
Published: July 2010

Recent developments in infrared (IR) spectroscopic time resolution, sensitivity and sample manipulation make this technique a powerful addition to the suite of complementary approaches for the study of time-resolved chemistry at metal centres within proteins. Application of IR spectroscopy to proteins has often targeted the amide bands as probes for gross structural change. This article focuses on the possibilities arising from recent IR technical developments for studies that monitor localized vibrational oscillators in proteins—native or exogenous ligands such as NO, CO, SCN
−
or CN
−
, or genetically or chemically introduced probes with IR-active vibrations. These report on the electronic and coordination state of metals, the kinetics, intermediates and reaction pathways of ligand release, hydrogen-bonding interactions between the protein and IR probe, and the electrostatic character of sites in a protein. Metalloprotein reactions can be triggered by light/dark transitions, an electrochemical step, a change in solute composition or equilibration with a new gas atmosphere, and spectra can be obtained over a range of time domains as far as the sub-picosecond level. We can expect to see IR spectroscopy exploited, alongside other spectroscopies, and crystallography, to elucidate reactions of a wide range of metalloprotein chemistry with relevance to cell metabolism, health and energy catalysis.
Towards nanomedicines: design protocols to assemble, visualize and test carbon nanotube probes for multi-modality biomedical imaging
Authors: Pascu Sofia I. , Arrowsmith Rory L. , Bayly Simon R. , Brayshaw Simon , Hu Zhiyuan
Published: July 2010

Nanomedicine is an interdisciplinary field, still in its infancy, where an accurate scientific assessment of potential risks and benefits is urgently needed, as is the engagement of end users and the public in this facet of the nanotechnology debate. There is increasing interest in improving our understanding of the interactions between nanomaterials and living systems, with regard to both the underlying chemistry and the physics of effects on the nanoscale. Ultimately, such knowledge promises new vistas for designing the ‘smart’ medicines of the future, of which targeted personalized drugs are the holy grail. Imaging and therapeutic components, including metallic radioisotopes, semiconductor quantum dots and magnetic materials, may be used to construct ‘nanocarriers’ (by encapsulation or conjugation) by rapid and simple (covalent and supramolecular) chemistry. The biomedical functions of the resulting materials are as yet largely unexplored. Encapsulation in nanocarriers could achieve delivery of the reagents (imaging and therapeutic drugs) to the sites of action in the body, while minimizing systemic toxicity and enzymatic degradation. These functional systems have the potential to become a general solution in drug delivery. Here we review recent developments concerning the applications of nanoparticles, including carbon nanotubes, as synthetic scaffolds for designing nanomedicines. This article will also focus on how understanding and design at the molecular level could help interdisciplinary teams develop research towards new diagnostics and therapeutics both in the short and the long term.
Invertebrate central pattern generator circuits
Authors: Selverston Allen I.
Published: July 2010

There are now a reasonable number of invertebrate central pattern generator (CPG) circuits described in sufficient detail that a mechanistic explanation of how they work is possible. These small circuits represent the best-understood neural circuits with which to investigate how cell-to-cell synaptic connections and individual channel conductances combine to generate rhythmic and patterned output. In this review, some of the main lessons that have appeared from this analysis are discussed and concrete examples of circuits ranging from single phase to multiple phase patterns are described. While it is clear that the cellular components of any CPG are basically the same, the topology of the circuits have evolved independently to meet the particular motor requirements of each individual organism and only a few general principles of circuit operation have emerged. The principal usefulness of small systems in relation to the brain is to demonstrate in detail how cellular infrastructure can be used to generate rhythmicity and form specialized patterns in a way that may suggest how similar processes might occur in more complex systems. But some of the problems and challenges associated with applying data from invertebrate preparations to the brain are also discussed. Finally, I discuss why it is useful to have well-defined circuits with which to examine various computational models that can be validated experimentally and possibly applied to brain circuits when the details of such circuits become available.
Phase-response curves and synchronized neural networks
Authors: Smeal Roy M. , Ermentrout G. Bard , White John A.
Published: July 2010

We review the principal assumptions underlying the application of phase-response curves (PRCs) to synchronization in neuronal networks. The PRC measures how much a given synaptic input perturbs spike timing in a neural oscillator. Among other applications, PRCs make explicit predictions about whether a given network of interconnected neurons will synchronize, as is often observed in cortical structures. Regarding the assumptions of the PRC theory, we conclude: (i) The assumption of noise-tolerant cellular oscillations at or near the network frequency holds in some but not all cases. (ii) Reduced models for PRC-based analysis can be formally related to more realistic models. (iii) Spike-rate adaptation limits PRC-based analysis but does not invalidate it. (iv) The dependence of PRCs on synaptic location emphasizes the importance of improving methods of synaptic stimulation. (v) New methods can distinguish between oscillations that derive from mutual connections and those arising from common drive. (vi) It is helpful to assume linear summation of effects of synaptic inputs; experiments with trains of inputs call this assumption into question. (vii) Relatively subtle changes in network structure can invalidate PRC-based predictions. (viii) Heterogeneity in the preferred frequencies of component neurons does not invalidate PRC analysis, but can annihilate synchronous activity.
Glial cells in neuronal network function
Authors: Araque Alfonso , Navarrete Marta
Published: July 2010

Numerous evidence demonstrates that astrocytes, a type of glial cell, are integral functional elements of the synapses, responding to neuronal activity and regulating synaptic transmission and plasticity. Consequently, they are actively involved in the processing, transfer and storage of information by the nervous system, which challenges the accepted paradigm that brain function results exclusively from neuronal network activity, and suggests that nervous system function actually arises from the activity of neuron–glia networks. Most of our knowledge of the properties and physiological consequences of the bidirectional communication between astrocytes and neurons resides at cellular and molecular levels. In contrast, much less is known at higher level of complexity, i.e. networks of cells, and the actual impact of astrocytes in the neuronal network function remains largely unexplored. In the present article, we summarize the current evidence that supports the notion that astrocytes are integral components of nervous system networks and we discuss some functional properties of intercellular signalling in neuron–glia networks.
Neuronal network analyses: premises, promises and uncertainties
Authors: Parker David
Published: July 2010

Neuronal networks assemble the cellular components needed for sensory, motor and cognitive functions. Any rational intervention in the nervous system will thus require an understanding of network function. Obtaining this understanding is widely considered to be one of the major tasks facing neuroscience today. Network analyses have been performed for some years in relatively simple systems. In addition to the direct insights these systems have provided, they also illustrate some of the difficulties of understanding network function. Nevertheless, in more complex systems (including human), claims are made that the cellular bases of behaviour are, or will shortly be, understood. While the discussion is necessarily limited, this issue will examine these claims and highlight some traditional and novel aspects of network analyses and their difficulties. This introduction discusses the criteria that need to be satisfied for network understanding, and how they relate to traditional and novel approaches being applied to addressing network function.
Beyond the wiring diagram: signalling through complex neuromodulator networks
Authors: Brezina Vladimir
Published: July 2010

During the computations performed by the nervous system, its ‘wiring diagram’—the map of its neurons and synaptic connections—is dynamically modified and supplemented by multiple actions of neuromodulators that can be so complex that they can be thought of as constituting a biochemical network that combines with the neuronal network to perform the computation. Thus, the neuronal wiring diagram alone is not sufficient to specify, and permit us to understand, the computation that underlies behaviour. Here I review how such modulatory networks operate, the problems that their existence poses for the experimental study and conceptual understanding of the computations performed by the nervous system, and how these problems may perhaps be solved and the computations understood by considering the structural and functional ‘logic’ of the modulatory networks.
Toward a theory of behavioral finance: implications from the natural sciences
Authors: Olsen Robert A.
Published: July 2010

Purpose

The purpose of this paper is to identify common inclusive concepts that might help define the boundaries of a general theory of behavioral finance.

Design/methodology/approach

A cross disciplinary review of relevant natural and social sciences is conducted to identify common foundational concepts.

Findings

The overall findings are that a general theory must include assumptions of subjective perception, indeterminacy, and a financial decision process that is both logical and affective.

Practical implications

Optimal financial decisions are not possible and significant market unpredictability will continue because of the dynamic complexity associated with disequilibrium.

Social implications

The current financial paradigm is based upon radically incorrect assumptions and a general theory of behavioral finance cannot arise from minor corrections to the current financial paradigm.

Originality/value

This paper is the first to attempt identifying foundational attributes of a behavioral financial paradigm.
Development of PCR-based codominant markers flanking the Alt3 gene in rye
Authors: Miftahudin  , Scoles G J , Gustafson J P
Published: July 2010

Aluminum (Al) toxicity is considered to be a major problem for crop growth and production on acid soils. The ability of crops to overcome Al toxicity varies among crop species and cultivars. Rye (Secale cereale L.) is the most Al-tolerant species among the Triticeae. Our previous study showed that Al tolerance in a rye F6 recombinant inbred line (RIL) population was controlled by a single gene designated as the aluminum tolerance (Alt3) gene on chromosome 4RL. Based on the DNA sequence of a rice (Oryza sativa L.) BAC clone suspected to be syntenic to the Alt3 gene region, we developed two PCR-based codominant markers flanking the gene. These two markers, a sequence-tagged site (STS) marker and a cleaved amplified polymorphic sequence (CAPS) marker, each flanked the Alt3 gene at an approximate distance of 0.4 cM and can be used to facilitate high-resolution mapping of the gene. The markers might also be used for marker-assisted selection in rye or wheat (Triticum aestivum L.) breeding programs to obtain Al-tolerant lines and (or) cultivars.Key words: rye, aluminum tolerance, CAPS, STS, flanking marker, rice BAC, synteny.
Linkage mapping of powdery mildew and greenbug resistance genes on recombinant 1RS from 'Amigo' and 'Kavkaz' wheat–rye translocations of chromosome 1RS.1AL
Authors: Mater Yehia , Baenziger Stephen , Gill Kulvinder , Graybosch Robert , Whitcher Lynda , Baker Cheryl , Specht James , Dweikat Ismail
Published: July 2010

Cultivated rye (Secale cereale L., 2n = 2x = 14, RR) is an important source of genes for insect and disease resistance in wheat (Triticum aestivum L., 2n = 6x = 42). Rye chromosome arm 1RS of S. cereale 'Kavkaz' originally found as a 1BL.1RS translocation, carries genes for disease resistance (e.g., Lr26, Sr31, Yr9, and Pm8), while 1RS of the S. cereale 'Amigo' translocation (1RSA) carries a single resistance gene for greenbug (Schizaphis graminum Rondani) biotypes B and C and also carries additional disease-resistance genes. The purpose of this research was to identify individual plants that were recombinant in the homologous region of.1AL.1RSVand 1AL.1RSAusing both molecular and phenotypic markers. Secale cereale 'Nekota' (1AL.1RSA) and S. cereale 'Pavon 76' (1AL.1RSV) were mated and the F1was backcrossed to 'Nekota' (1AL.1AS) to generate eighty BC1F2:3families (i.e., ('Nekota' 1AL.1RSA× 'Pavon 76' 1AL.1RSV) × 'Nekota' 1AL.1AS). These families were genotyped using the secalin–gliadin grain storage protein banding pattern generated with polyacrylamide gel electrophoresis to discriminate 1AL.1AS/1AL.1RS heterozygotes from the 1AL.1RSA+Vand 1AL.1AS homozygotes. Segregation of the secalin locus and PCR markers based on the R173 family of rye specific repeated DNA sequences demonstrated the presence of recombinant 1AL.1RSA+Vfamilies. Powdery mildew (Blumeria graminis) and greenbug resistance genes on the recombinant 1RSA+Varm were mapped in relation to the Sec-1 locus, 2 additional protein bands, 3 SSRs, and 13 RFLP markers. The resultant linkage map of 1RS spanned 82.4 cM with marker order and spacing showing reasonable agreement with previous maps of 1RS. Fifteen markers lie within a region of 29.7 cM next to the centromere, yet corresponded to just 36% of the overall map length. The map position of the RFLP marker probe mwg68 was 10.9 cM distal to the Sec-1 locus and 7.8 cM proximal to the powdery mildew resistance locus. The greenbug resistance gene was located 2.7 cM proximal to the Sec-1 locus.Key words: microsatellites, SSRs, RFLP, secalin-gliadin, alien genes introgression.
Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean
Authors: McClean Phillip E , Lee Rian K , Miklas Phillip N
Published: July 2010

Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (π/bp) was 0.0481, a value higher than that reported for introns from other plant species. Tests for significant deviation from the mutation drift model were positive for the population as a whole, the cultivar and landrace subsets, and the Middle American landrace set. Significant linkage disequilibrium extended about 300 nucleotides. Twenty haplotypes were detected among the cultivated genotypes. Seven recombination events were detected for the whole population, and six events for the landraces. Recombination was not observed among the landraces within either the Middle American or Andean gene pools. Evidence for hybridization between the two gene pools was discovered. Five allele-specific primers were developed that could distinguish 56 additional genotypes. The allele-specific primers were used to map duplicate DFR genes on linkage group B8.Key words: Phaseolus vulgaris, intron, diversity, evolution.
Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)
Authors: Qian Yaping , Jin Li , Su Bing
Published: July 2010

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey (Ateles geoffroyi). A total of 193 152 BAC clones were generated in this library. The average insert size of the BAC clones was estimated to be 184.6 kb with the small inserts (50-100 kb) accounting for less than 3% and the non-recombinant clones only 1.2%. Assuming a similar genome size with humans, the spider monkey BAC library has about 11× genome coverage. In addition, by end sequencing of randomly selected BAC clones, we generated 367 sequence tags for the library. When blasted against human genome, they showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the library. This black-handed spider monkey BAC library would serve as a valuable resource in comparative genomic study and large-scale genome sequencing of nonhuman primates.Key words: black-handed spider monkeys, Ateles geoffroyi, BAC library.
A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome
Authors: Russell Joanne , Booth Allan , Fuller John , Harrower Brian , Hedley Peter , Machray Gordon , Powell Wayne
Published: July 2010

Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion–deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.Key words: SNPs, haplotype, SSRs, barley.
Amplified fragment length polymorphism linkage analysis of common buckwheat (Fagopyrum esculentum) and its wild self-pollinated relativeFagopyrum homotropicum
Authors: Yasui Yasuo , Wang Yingjie , Ohnishi Ohmi , Campbell Clayton G
Published: July 2010

Common buckwheat (Fagopyrum esculentum) (2n = 2x = 16) and Fagopyrum homotropicum (2n = 2x = 16) were mated in an interspecific cross and amplified fragment length polymorphism (AFLP) linkage maps were constructed by analyzing segregation in the F2population. Six hundred and sixty-nine bands were identified using 20 AFLP primer combinations, of which 462 (69%) segregated in the F2population. The map of F. esculentum has eight linkage groups with 223 markers covering a total of 508.3 cM. The map of F. homotropicum has eight linkage groups with 211 markers covering 548.9 cM. There was one to one correspondence of the esculentum and homotropicum linkage groups. Three morphological markers, distylous self-incompatibility, shattering habit, and winged seed, were located on the AFLP map. Distylous self-incompatibility and shattering habit are tightly linked to each other (1.3 cM) and are located near the center of linkage group 1. Winged seed is located on linkage group 4. Key words: common buckwheat, AFLP, linkage analysis, distylous self-incompatibility, shattering habit.
Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS–PCR
Authors: Chiapparino E , Lee D , Donini P
Published: July 2010

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS–PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.Key words: single nucleotide polymorphisms (SNPs), genotyping, barley, tetra-primers ARMS–PCR.
Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species
Authors: Bardini Mauro , Lee David , Donini Paolo , Mariani Anna , Gianì Silvia , Toschi Marcello , Lowe Chris , Breviario Diego
Published: July 2010

TBP (tubulin-based polymorphism) is a new molecular marker based tool that relies on the presence of intron-specific DNA polymorphisms of the plant β-tubulin gene family. The multifunctional and essential role of the tubulin proteins is reflected in the conservation of regions within their primary amino acid sequence. The ubiquitous nature of this gene family can be exploited using primers that amplify the first intron of different β-tubulin isotypes, revealing specific fingerprints. The method is rapid, simple, and reliable and does not require preliminary sequence information of the plant genome of interest. The ability of TBP to discriminate between accessions and species in oilseed rape, coffee, and lotus is shown. In all cases, TBP was able to detect specific genetic polymorphisms in the context of a simplified and readily appreciable pattern of DNA amplification. The application of TBP for assessing genetic diversity and genome origins in disseminated plant landraces rather than in highly inbred cultivated species is also discussed.Key words: β-tubulin, Brassica napus, Coffea, Lotus, SSRs.
Isolation and inheritance of microsatellite loci in the Dungeness crab (Brachyura: Cancridae: Cancer magister)
Authors: Jensen Pamela C , Bentzen Paul
Published: July 2010

The isolation, PCR amplification, and descriptive statistics of six microsatellite loci are described for the Dungeness crab, Cancer magister. Also reported is the inheritance of these loci in two families obtained from artificial crosses in the laboratory. All six loci conform to expectations under Mendelian inheritance and there is no evidence for linkage between any of the loci. Allelic size ranges for three of the loci are relatively large, ranging from 135–357 bp between the smallest and largest allele detected at that locus. At two of these loci upper allelic drop out (non-amplification of the larger allele in a heterozygous individual) can be problematic for scoring. Results from cross-species amplification in nine congeners are summarized. These loci will be valuable in studies requiring high-resolution genetic markers in Dungeness crabs and related species.Key words: Cancer magister, microsatellite, Mendelian Inheritance, cross species amplification, Brachyura.
Cytology ofWolbachia-induced parthenogenesis inLeptopilina clavipes(Hymenoptera: Figitidae)
Authors: Pannebakker Bart A , Pijnacker Laas P , Zwaan Bas J , Beukeboom Leo W
Published: July 2010

Parthenogenesis induced by cytoplasmatically inherited Wolbachia bacteria has been found in a number of arthropod species, mainly Hymenoptera. Previously, two different forms of diploidy restoration have been reported to underlie parthenogenesis induction in Hymenoptera by Wolbachia. Both are a form of gamete duplication, but each differs in their timing. We investigated the cytology of the early embryonic development of a Wolbachia-infected strain of the parasitoid wasp Leptopilina clavipes and compared it with that of an uninfected sexual strain. Both strains have a similar meiosis. In the infected parthenogenetic strain, diploidy is restored by anaphase restitution during the first somatic mitosis, similar to Trichogramma, but not to Muscidifurax. Our results confirm the occurrence of different cytological mechanisms of diploidy restoration associated with parthenogenesis-inducing Wolbachia in the order Hymenoptera.Key words: gamete duplication, Leptopilina clavipes, parthenogenesis, thelytoky, Wolbachia.
Effect of 5-azacytidine and trichostatin A on somatic centromere association in wheat
Authors: Vorontsova Maria , Shaw Peter , Reader Steve , Moore Graham
Published: July 2010

Both homologous and non-homologous chromosomes in wheat associate via their centromeric hetero chromatin in the developing xylem vessel cells of the root. The antimetabolite 5-azacytidine (which reduces DNA methylation) decreases the overall level of centromere association. Treatment with 5-azacytidine caused a more marked reduction in the level of homologous chromosome association observed in a wheat line carrying a pair of marked chromosomes. On the other hand, treatment of wheat seedlings with trichostatin A (which increases histone acetylation) raises the overall level of centromere association. The Ph1 locus controls the specificity of both somatic and meiotic pairing of homologous centromeres in wheat. The level of non-homologously associated centromeres is, however, reduced in the presence of Ph1 compared with its absence, even after treatment with either drug. Thus these two drugs, which have been shown to affect chromatin structure, do affect chromosome association, but Ph1 must act at least in part by a different mechanism.Key words: pairing, roots, cereals, Ph1, polyploids.
Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis meloL.)
Authors: Morales M , Roig E , Monforte A J , Arús P , Garcia-Mas J
Published: July 2010

A search was performed for single-nucleotide polymorphisms (SNP) and short insertions–deletions (indels) in 34 melon (Cucumis melo L.) expressed sequence tag (EST) fragments between two distantly related melon genotypes, a group Inodorus 'Piel de sapo' market class breeding line T111 and the Korean accession PI 161375. In total, we studied 15 kb of melon sequence. The average frequency of SNPs between the two genotypes was one every 441 bp. One indel was also found every 1666 bp. Seventy-five percent of the polymorphisms were located in introns and the 3′ untranslated regions. On average, there were 1.26 SNPs plus indels per amplicon. We explored three different SNP detection systems to position five of the SNPs in a melon genetic map. Three of the SNPs were mapped using cleaved amplified polymorphic sequence (CAPS) markers, one SNP was mapped using the single primer extension reaction with fluorescent-labelled dideoxynucleotides, and one indel was mapped using polyacrilamide gel electrophoresis separation. The discovery of SNPs based on ESTs and a suitable system for SNP detection has broad potential utility in melon genome mapping.Key words: SNP, CAPS marker, single primer extension.