bluuebunny/crossref_metadata_2025 huggingface dataset:
Democratic Transactions in the Life Sciences
Authors: Huijer Marli , Janze Irene
Published: December 2004

This article presents an artistic and political experiment as an effort to advance democratic transactions in the life sciences. Artists built a ‘gender democratic labyrinth’ in Maastricht, in which scientists, women’s groups, people in general, artists, philosophers, politicians, journalists, clinical geneticists and many others interacted and negotiated on the creation of human embryos for medical-scientific research (a subject kept open in the Dutch Embryo Law of September 2002 to decide within a few years). By taking a gender perspective on the process of democratizing science, we aimed to create a space in which alterity and difference are constitutive elements in the public exchanges on science and technology. The idea to build a labyrinth was theoretically based on the notion of agonistic democracy - in which pluralism is the result of contestations and divisions - and on a notion of science and technology as being contextualized and socialized.
Violence against Prostitutes
Authors: Ribeiro Manuela , Sacramento Octávio
Published: December 2004

Violence has long been assumed to be an intrinsic trait of female prostitution. However, it has been mostly associated with the locale in which the activity is exercised, i.e. with working time and space. In this article, based on data gathered by direct observations, in-depth interviews and the compilation of so-called time-budgets, the authors demonstrate that violence is as pervasive and omnipresent a feature of prostitutes’ ostensibly private ‘off-duty’ (non-working) time and space, though it takes on varied and distinct forms and configurations, compared to violence in the workplace.
Imagining Gendered Adulthood
Authors: Gordon Tuula , Holland Janet , Lahelma Elina , Thomson Rachel
Published: December 2004

In this article, the authors draw on two qualitative, longitudinal studies of young people’s transitions to adulthood and how they construct these transitions over time in social, cultural and material terms. The authors focus on the hopes, anxieties and imagined futures of young women. They discuss the individualization thesis, and the contradiction for female individualization between expectations of equality and the reality of inequality between the genders. The debate is moved beyond ‘pitiful girls’ and ‘can-do girls’ by exploring how young women in the UK and Finland anticipate and try to avoid being locked into the lives of adult women.
Perceptions of Self and Group in the Context of a Threatened National Identity: A Field Study
Authors: Cameron James E. , Duck Julie M. , Terry Deborah J. , Lalonde Richard N.
Published: December 2004

Previous research indicates that people who are highly identified with their groups tend to remain committed to them under threat. This study examines the generalizability of this effect to (a) a real-life context involving the perception that others view the ingroup (Australians) as intolerant of minorities and (b) various dimensions of social identification. The sample comprised 213 respondents to a random mail survey. Perceived threat was inversely related to self-stereotyping (i.e. perceptions of self-ingroup similarity), but only for individuals with weak subjective ties to other group members. Threat perceptions were also predictive of enhanced judgments of within-group variability on threat-relevant dimensions, particularly for individuals with weaker ingroup ties. Various strategies for coping with a threatened social identity are linked to different facets of social identification.
Rethinking tourism
Authors: McRae Leanne
Published: December 2004

Tourist studies explores the movement of people through spaces. A key theme within the paradigm is to revision the relationships between tourists and hosts. This article mobilizes postcolonial critic Edward Said’s understandings of space, exile and ambiguity to refigure the unclear moments and meanings activated when tourists and hosts meet.

By mobilizing Said it is hoped to reveal a more fluid and flexible rendering of the tourist discourse as it is mobilized through places - both physical and imagined. Tourists and hosts both reaffirm and transgress these places to redefine the possibilities in the meeting of different bodies, minds, cultures, practices and politics.
Images of Israel
Authors: Cohen Erik H.
Published: December 2004

A multidimensional analysis of Jewish youth tour participants’ responses to symbols of Israel identified four types of destination images: spiritual, Zionist, pragmatic/mundane and home. Their responses are analyzed along national, gender, denominational and ethnic lines. Two main groupings were found: those indicating a strongly spiritual and religious view of Israel and those indicating a more diverse image of daily life in the modern State of Israel. The strongest influence on destination image appears to be country of residence. Differential influences are related to the host culture, educational system and relative exposure to ‘complex’ destination images from past personal experience.
On the uses of travel guides in the context of German tourism to Scotland
Authors: Jack Gavin , Phipps Alison
Published: December 2004

Travel guides are a paradigmatic form of modern travel writing. Recent historical and textual analyses of guides regard them as sites of ideological struggle and indices of shifting cultural understandings about the purpose and nature of travel itself. This article builds upon this text-based research by using ethnographic data to explore the functions and uses of guides in the everyday life of tourism before, during and after actual travel. We place particular focus on exploring guides as forms of apodemic literature1, that is as didactic literature that has important performative and agentic functions. We consider the ways that actual tourists use these guides to do important identity-work and pay particular attention to the historical and sociological specificities of German tourism to Scotland in substantiating this. We conclude by suggesting that travel guides perform important ontological as well as epistemological roles for tourists and that as an artefact of modern culture, their use can also be interpreted in liminal terms when articulated against the wider connections between Modernity, life and death.
When is a tourist?
Authors: O’Reilly Karen
Published: December 2004

As flexible forms of migration undermine the distinction between tourism and migration, analyses of human mobility demand new conceptualizations and characterizations. However, before we rush to ever more metaphors of flux and flow it is important to explore the articulation of tourism and migration as they are experienced in individuals’ daily lives. This article draws on ethnographic data to investigate in depth the migration experiences of three forms of tourism-related migration of British migrants in Spain: retirement migrants, entrepreneurial migrants, and consumption-led economically-active migrants. We note that these migration patterns are inextricably linked to tourism history and tourist systems, and via individual actions, attitudes and expectations. We also note that theories of tourism as escape can illuminate the behaviour of some of the migrants. However, we acknowledge that these migrants cannot, therefore, be considered to be tourists. In crucial definitional ways they are migrants. Furthermore, they claim not to be tourists. The article then goes on to explore how the articulation of migration and tourism can be a tension for some groups of migrants who are uncomfortable with constant flux. Articulation enables us to explore the two things that articulate as separate entities and the joint, or nexus, and how this joining together, this articulation, is experienced by diverse groups of mobile humans.
An Improved Approach for Synthesis of Positively Charged Silver Nanoparticles
Authors: Sui Zhenming , Chen Xiao , Wang Luyan , Chai Yongcun , Yang Chunjie , Zhao Jikuan
Published: December 2004

Positively charged silver nanoparticles capped by cetyltrimethyl ammonium bromide (CTAB) are prepared in aqueous solution. The structure of capping agents on Ag particles is systematically characterized by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and thermal gravimetric analysis (TGA). It suggests that CTAB molecules form a bilayer shell on Ag surface with a 1:5 rough ratio of inner/outer molecules.
A Helical Supramolecular Polymer Formed by Host–Guest Interactions
Authors: Miyauchi Masahiko , Harada Akira
Published: December 2004

3-[4-(tert-Boc-amino)cinnamoylamino]-α-cyclodextrin (3-4-tBocCiNH-α-CD) has been found to form a supramolecular polymer in an aqueous solution. The supramolecular polymer was found to take a helical structure. This is the first example of the formation of a helical supramolecular polymer formed by host–guest interactions.
Lyophilization of Lipase Together with Ionic Compounds Generates Highly Enantioselective and Solvent-sensitive Lipase in Organic Solvents
Authors: Ueji Shin-ichi , Mori Shu-ichi , Yumoto Hiromi , Hiroshima Naomi , Ebara Yasuhito
Published: December 2004

The lyophilization of lipase from aqueous enzyme solution containing ionic compounds such as disodium hydrogenphosphate resulted in a dramatic improvement of its enantioselectivity for esterification in organic solvents, compared with the ionic compound-free lipase. The enantioselectivity of the ionic compound-coated lipase was found to be fairly sensitive to the change of the solvents.
Fabrication of Silver Nanowires by Selective Electroless Plating of DNA Stretched Using the LB Method
Authors: Hashimoto Yuichi , Matsuo Yasutaka , Ijiro Kuniharu
Published: December 2004

Precise and uniform metallization of double-stranded DNA by the selective electroless plating method was investigated for the fabrication of nanowires. Cis-platin was bound to template DNA molecules and reduced to platinum which then catalyzed silver metal deposition. The DNA molecules combined with the platinum clusters were stretched and immobilized on a glass substrate using the Langmuir–Blodgett (LB) method. The electroless plating of the platinum-bound DNA molecules by the reduction of silver ions yielded uniform silver nanowires (ca. 50 nm in width and height) along the stretched DNA molecules. Conductive AFM measurements revealed that a high electric conductivity over a length of 6 μm from the edge of a micro electrode.
A Novel Gallium/Samarium-mediated Coupling of Epoxides with Allyl Halides in Aqueous Media and Synthesis of Homoallylic Alcohols
Authors: Gohain Mukut , Prajapati Dipak
Published: December 2004

A mild and efficient protocol for the coupling of various substituted epoxides 1 with allylgallium reagent generated in situ in a Bu4NBr–DMF–H2O system have been developed. The coupling is also found to be equally effective when samarium is used in lieu of gallium and the corresponding homoallylic alcohols 2 were obtained in almost comparable yields.
Surfactant-dependent Photoluminescence of CdTe Nanocrystals in Aqueous Solution
Authors: Li Chunliang , Murase Norio
Published: December 2004

Photoluminescence (PL) efficiency of CdTe nanocrystals was investigated as a function of the ratio of surfactant (thioglycolic acid, TGA) to Cd2+ used in aqueous preparation. When the ratio was 1.3, a maximum PL efficiency of 65% was obtained. Within our knowledge, this value is the highest ever reported for as-prepared aqueous solution. Surfactants added more than the optimal amount tend to gather densely on the nanocrystals, and distort the surface. This might be one explanation of the decrease of efficiency.
Sonochemical Synthesis of Inorganic–Organic Hybrid Nanocomposite Based on Gold Nanoparticles and Polypyrrole
Authors: Park Jong-Eun , Atobe Mahito , Fuchigami Toshio
Published: December 2004

Colloidal dispersions of hybrid nanocomposite composed of gold nanoparticles (Au-NPs) and polypyrrole (PPy) were prepared by a sonochemical method, in which gold ion and pyrrole monomer in an aqueous solution were reduced and oxidized, respectively, by ultrasonic irradiation in the presence of poly(N-vinyl-2-pyrrolidone) (PVP).
High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation
Authors: MOCHIZUKI KIYOTAKA , OGURO AKIHIRO , OHTSU TAKASHI , SONENBERG NAHUM , NAKAMURA YOSHIKAZU
Published: December 2004

The eukaryotic translation initiation factor 4F (eIF4F) consists of three polypeptides (eIF4A, eIF4G, and eIF4E) and is responsible for recruiting ribosomes to mRNA. eIF4E recognizes the mRNA 5′-cap structure (m7GpppN) and plays a pivotal role in control of translation initiation, which is the rate-limiting step in translation. Overexpression of eIF4E has a dramatic effect on cell growth and leads to oncogenic transformation. Therefore, an inhibitory agent to eIF4E, if any, might serve as a novel therapeutic against malignancies that are caused by aberrant translational control. Along these lines, we developed two RNA aptamers, aptamer 1 and aptamer 2, with high affinity for mammalian eIF4E by in vitro RNA selection-amplification. Aptamer 1 inhibits the cap binding to eIF4E more efficiently than the cap analog m7GpppN or aptamer 2. Consistently, aptamer 1 inhibits specifically cap-dependent in vitro translation while it does not inhibit cap-independent HCV IRES-directed translation initiation. The interaction between eIF4E and eIF4E-binding protein 1 (4E-BP1), however, was not inhibited by aptamer 1. Aptamer 1 is composed of 86 nucleotides, and the high affinity to eIF4E is affected by deletions at both termini. Moreover, relatively large areas in the aptamer 1 fold are protected by eIF4E as determined by ribonuclease footprinting. These findings indicate that aptamers can achieve high affinity to a specific target protein via global conformational recognition. The genetic mutation and affinity study of variant eIF4E proteins suggests that aptamer 1 binds to eIF4E adjacent to the entrance of the cap-binding slot and blocks the cap-binding pocket, thereby inhibiting translation initiation.
Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy
Authors: KISSELEVA NATALIA , KHVOROVA ANASTASIA , WESTHOF ERIC , SCHIEMANN OLAV
Published: December 2004

Electron paramagnetic resonance (EPR) spectroscopy is used to study the binding of MnII ions to a tertiary stabilized hammer-head ribozyme (tsHHRz) and to compare it with the binding to the minimal hammerhead ribozyme (mHHRz). Continuous wave EPR measurements show that the tsHHRz possesses a single high-affinity MnII binding site with a KD of ≤10 nM at an NaCl concentration of 0.1 M. This dissociation constant is at least two orders of magnitude smaller than the KD determined previously for the single high-affinity MnII site in the mHHRz. In addition, whereas the high-affinity MnII is displaced from the mHHRz upon binding of the aminoglycoside antibiotic neomycin B, it is not from the tsHHRz. Despite these pronounced differences in binding, a comparison between the electron spin echo envelope modulation and hyperfine sublevel correlation spectra of the minimal and tertiary stabilized HHRz demonstrates that the structure of both binding sites is very similar. This suggests that the MnII is located in both ribozymes between the bases A9 and G10.1 of the sheared G · A tandem base pair, as shown previously and in detail for the mHHRz. Thus, the much stronger MnII binding in the tsHHRz is attributed to the interaction between the two external loops, which locks in the RNA fold, trapping the MnII in the tightly bound conformation, whereas the absence of long-range loop–loop interactions in the mHHRz leads to more dynamical and open conformations, decreasing MnII binding.
Analysis of 2′-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: Evidence for a conserved two-step reaction mechanism
Authors: STEIGER MICHELLE A. , JACKMAN JANE E. , PHIZICKY ERIC M.
Published: December 2004

Tpt1p is an essential protein responsible for the 2′-phosphotransferase step of tRNA splicing in Saccharomyces cerevisiae, in which the splice junction 2′-phosphate of ligated tRNA is transferred to NAD to form mature tRNA and ADP-ribose 1″-2″ cyclic phosphate. We showed previously that Tpt1p is a member of a family of functional 2′-phosphotransferases found in eukaryotes, eubacteria, and archaea, that the Escherichia coli protein (KptA) is highly specific for 2′-phosphorylated RNAs despite the lack of obvious natural substrates, and that KptA acts on a trinucleotide substrate through an intermediate in which RNA is ADP-ribosylated at the 2′-phosphate. This mechanism is similar to a proposed mechanism of NAD-dependent histone deacetylases. We present evidence here that this mechanism is conserved in S. cerevisiae, and we identify residues important for the second step of the reaction, during which the intermediate is resolved into products. We examined 21 Tpt1 protein variants mutated in conserved residues or blocks of residues and show that one of them, Tpt1 K69A/R71S protein, accumulates large amounts of intermediate with trinucleotide substrate due to a very slow second step. This intermediate can be trapped on beads when formed with biotin-NAD. We also show that Tpt1 K69A/R71S protein forms an intermediate with the natural ligated tRNA substrate and demonstrate that, as expected, this mutation is lethal in yeast. The high degree of conservation of these residues suggests that the entire Tpt1p family is involved in a similar two-step chemical reaction.
A nomenclature for all signal recognition particle RNAs
Authors: ZWIEB CHRISTIAN , VAN NUES ROB W. , ROSENBLAD MAGNUS ALM , BROWN JEREMY D. , SAMUELSSON TORE
Published: December 2004

The signal recognition particle (SRP) is a cytosolic ribonucleoprotein complex that guides secretory proteins to biological membranes in all organisms. The SRP RNA is at the center of the structure and function of the SRP. The comparison of the growing number of SRP RNA sequences provides a rich source for gaining valuable insight into the composition, assembly, and phylogeny of the SRP. In order to assist in the continuation of these studies, we propose an SRP RNA nomenclature applicable to the three divisions of life.
Twinsvs. modular crystal structures
Authors: Nespolo Massimo , Ferraris Giovanni , Ďurovič Slavomil , Takéuchi Yoshio
Published: December 2004

The crystallographic nature of modular structures is analysed and discussed in terms of their symmetry and structure building operations. The modular crystal structures we discuss in this paper are homogeneous edifices, built by one or more types of modules related by a point-space operation, and the whole structure is described by an ordinary three-dimensional triperiodic space group. Because the term “twin” is often used, with or without modifiers, to describe symmetry operations that act as building mechanisms in modular structures, a comparison is made with twins, that are instead heterogeneous edifices, described not by a space group but by a (polychromatic) point group, where the individuals are related by operations in the vector space. A unifying scheme is proposed where the passage from heterogeneous to homogeneous structures, only apparently justified by a change of dimensions of the individuals, implies a change of space where the operations are defined.
Renewed interest in powder diffraction data indexing
Authors: Bergmann Jörg , Le Bail Armel , Shirley Robin , Zlokazov Victor
Published: December 2004

Recently released powder indexing programs are reviewed and placed in competition with the established programs (ITO, TREOR, DICVOL, etc.) through a series of problems selected among previously unindexed ICDD entries designated as “high quality”. Benchmarks are provided for testing indexing programs, based on the bethanechol chloride powder diffraction data. Applying these benchmarks leads to a classification (with respect to this specific example) of indexing programs as they face progressively more difficult situations. High data quality and the user experience to obtain it are concluded to remain the best way to indexing success, given that nearly all programs produce excellent results with excellent data. Lack of attention to data quality, even if followed by use of the most efficient programs, will usually lead to failure. It is demonstrated how not restricting oneself to a single indexing program can considerably increase the chances of success.
Exploiting texture to estimate the relative intensities of overlapping reflections
Authors: Baerlocher Christian , McCusker Lynne B. , Prokic Sinisa , Wessels Thomas
Published: December 2004

Additional information about the relative intensities of reflections that overlap in a powder diffraction pattern can be obtained from a polycrystalline sample in which the crystallites are preferentially oriented. If the data are collected and analyzed appropriately, more single-crystal-like reflection intensities can be extracted, and thereby more complex structures solved. This ‘texture method’ was implemented initially in reflection mode and its power demonstrated with the solution of the 117-atom structure of the high-silica zeolite UTD-1F. However, the experiment required a minimum of 3 days of synchrotron beamtime per sample. In an attempt to reduce the amount of beamtime needed and to simplify the experiment itself, a transmission mode alternative using an area detector was developed. Details of the sample preparation, data collection and data analysis for both geometries are described. The solution of the structures of the aluminophosphates Mu-9 (R3̅c,a= 14.0696(1) Å,c= 42.3113(4) Å) and AlPO-M (Pbca,a= 9.7493(1) Å,b= 29.1668(2) Å,c= 9.3528(1) Å) using reflection and transmission mode data, respectively, are provided as examples of the method.
Multicrystal approach to crystal structure solution and refinement
Authors: Vaughan Gavin B. M. , Schmidt Soeren , Poulsen Henning F.
Published: December 2004

We present a method in which the contributions from the individual crystallites in a polycrystalline sample are separated and treated as essentially single crystal data sets. The process involves the simultaneous determination of the orientation matrices of the individual crystallites in the sample, the subsequent integration of the individual peaks, and filtering and summing of the subsequent integrated intensities, in order to arrive at a single-crystal like data set which may be treated normally. In order to demonstrate the method, we consider as a test case a small molecule structure, cupric acetate monohyrade. We show that it is possible to obtain a single-crystal quality structure solution and refinement, in which accurate anisotropic thermal parameters and hydrogen atom positions are obtained.
Advances and some recent applications of the origin-free modulus sum function
Authors: Rius Jordi
Published: December 2004

Since its discovery, the direct methods origin-free modulus sum function [Rius, J., Acta Cryst A49 (1993) 406—409] has been responsible for the solution of a number of difficult crystal structures of minerals and other inorganic compounds from powder diffraction data. This is principally due to the efficiency, robustness and simplicity of implementation of this phase refinement function. The first part of the contribution describes some recent examples on the application of the origin-free modulus sum function to complex structures. In the second part, a powerful variant of this function is introduced which discriminates even better the correct solutions from the wrong ones. This is illustrated with its application to single-crystal data of three selected organic structures. One of these test structures contains 317-atom molecules and is regarded as one of the most difficult structures to be solved with reciprocal space direct methods. This variant could also be useful for those phase refinement strategies based on alternating reciprocal- and real-space procedures, provided that the weak reflections are known.
A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction
Authors: Favre-Nicolin Vincent , Černý Radovan
Published: December 2004

Ab initio structure determination using direct-space methods, although relying on an essentially brute-force approach, can be greatly improved through smarter algorithms. The most basic improvement involves the use of prior information to reduce the number of configurations evaluated to find the structure solution. It is however vitally important that the parametrization used to incorporate this prior information does not reduce the efficiency with which the configuration space is explored. We will show that this can be achieved by defining molecules and polyhedra through a set of restraints associated to dedicated random changes, allowing to solve structures up to three times as fast as with the ‘standard’ approach where atomic positions are parametrized directly from bond lengths, bond angles and dihedral angles.

To further enhance the efficiency of the algorithm, it is also possible to ‘tune’ the convergence criterion used to compare the structural model to the observed diffraction data (usually χ
2 or Rwp
). By using Maximum Likelihood principles, it is shown that incorporating the fact that the model is approximate in the χ
2 evaluation can improve the algorithm convergence towards the structure solution.
Structure solution of zeolites from powder diffraction data
Authors: Burton Allen W.
Published: December 2004

This article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.Ab initiostructure determination of zeolites from powder data has made great progress within the past 10 years. In particular, the developments of the ZEFSAII, FOCUS, and XLENS algorithms have allowed rapid structure solutions of zeolites, in some cases a few days after their initial discoveries.
Structure determination of thermal decomposition products from laboratory X-ray powder diffraction
Authors: Bataille Thierry , Audebrand Nathalie , Boultif Ali , Louër Daniel
Published: December 2004

Ab initio structure determination from powder diffraction data of compounds resulting from solid state transformations is still rather limited. Two major factors influence the stages of the structure elucidation of these solids, i.e. the lower precision in peak position for indexing and the strong line overlap for extracting integrated intensities. The present study deals with the consideration of these two problems for solving the crystal structure of two thermal-decomposition inorganic products, Nd(NO3)3 · 4 H2O and Pb3O2(NO3)2. The new features of DICVOL04, as zero shift refinement, a priori zero search and tolerance of spurious lines have been used for indexing several phases obtained during the thermal treatment of neodymium nitrate hexahydrate. The crystal structures of Nd(NO3)3 · 4 H2O and Pb3O2(NO3)2 have been solved with the direct methods and the structure model of Pb3O2(NO3)2 has been completed using a global optimisation approach. The monoclinic structure of neodymium nitrate tetrahydrate [a = 10.1744(4) Å, b = 8.9716(5) Å, c = 11.7295(5) Å, β = 97.384(4)°, V = 1061.80 Å3, S.G. P21/c] is built from isolated ten-fold coordinated Nd polyhedra. The orthorhombic structure of lead oxide nitrate [a = 7.6034(4) Å, b = 5.7691(4) Å, c = 18.5817(9) Å, V = 815.09 Å3, S.G. Pnma] is built from double chains of edge-sharing OPb4 tetrahedra connected by nitrate groups. In order to estimate the chance of solving crystal structure of nanocrystalline powdered compounds, a comparison of the efficiency of direct methods and direct-space approaches is made from powder diffraction patterns simulated for various crystallite sizes from the crystal structure of the decomposition product γ-Zn2P2O7.
Studying the structure of metal-organic polymers using in-house powder X-ray diffraction data: structural transformations induced by thermal treatment
Authors: Neels Antonia , Wang Yi , Stoeckli-Evans Helen
Published: December 2004

The use of X-ray powder diffraction for the structure determination of inorganic, organic and metal-organic compounds has grown impressively over the last ten years. In supramolecular chemistry, the knowledge of the three-dimensional structure of a material is essential for the discussion of its macroscopic behaviour, and as a result the design of new functionalized materials.

The ab initio crystal structure determination of previously unknown metal-organic compounds is still rare but is a field of high interest and activity. Here we describe the formation of 1D coordination polymers and the phase transformation processes that lead to the formation of 3D polymers on heating, accompanied by colour changes.

The reaction of pyrazine-2,5-dimethyl-3,6-dicarboxylic acid with first row transition metal salts lead to the formation of coordination polymers always in the form of microcrystalline powders. With manganese and nickel salts isostructural 1D coordination polymers were obtained. With zinc chloride and copper chloride isomorphous 1D coordination polymers were obtained. The thermal decomposition of the nickel and copper polymers were studied and it was shown that on the loss of the coordinated water molecules new 3D coordination polymers could be obtained. In both the 1D and 3D coordination polymers the metal atoms have octahedral geometry in N2O4 environments. The crystal structures of all six complexes have been determined from powder X-ray diffraction data. Crystal data: (1) crystal symmetry monoclinic [space group P21/c, a = 7.4645(1), b = 8.9472(2), c = 7.6166(1) Å, β = 92.198(2)°]; (2) crystal symmetry orthorhombic [space group Pmna, a = 7.4060(2), b = 7.1857(2), c = 9.0661(2) Å]; (3) crystal symmetry monoclinic [space group P21/c, a = 6.9376(9), b = 7.1306(12), c = 8.5852(20) Å, β = 113.299(18)°]; (4) crystal symmetry orthorhombic [space group Pbcn, a = 9.0593(2), b = 7.4410(1), c = 14.6697(2) Å]; (5) crystal symmetry orthorhombic [space group Pbcn, a = 8.9727(1), b = 7.2354(1), c = 15.0444(2) Å]; (6) crystal symmetry monoclinic [space group P21/c, a = 6.9133(4), b = 7.9927(6), c = 8.2084(6) Å, β = 110.066(6)°].
A Separation-of-Timescales Approach to the Coalescent in a Continuous Population
Authors: Wilkins Jon F
Published: December 2004

This article presents an analysis of a model of isolation by distance in a continuous, two-dimensional habitat. An approximate expression is derived for the distribution of coalescence times for a pair of sequences sampled from specific locations in a rectangular habitat. Results are qualitatively similar to previous analyses of isolation by distance, but account explicitly for the location of samples relative to the habitat boundaries. A separation-of-timescales approach takes advantage of the fact that the sampling locations affect only the recent coalescent behavior. When the population size is larger than the number of generations required for a lineage to cross the habitat range, the long-term genealogical process is reasonably well described by Kingman's coalescent with time rescaled by the effective population size. This long-term effective population size is affected by the local dispersal behavior as well as the geometry of the habitat. When the population size is smaller than the time required to cross the habitat, deep branches in the genealogy are longer than would be expected under the standard neutral coalescent, similar to the pattern expected for a panmictic population whose population size was larger in the past.
Robust Transmission/Disequilibrium Test for Incomplete Family Genotypes
Authors: Sebastiani Paola , Abad Maria M , Alpargu Gülhan , Ramoni Marco F
Published: December 2004

Several solutions have been proposed to extend the transmission disequilibrium test (TDT) to include cases with missing parental genotype. However, completion of the missing parental genotype may bias the test if the underlying missing data mechanism is informative. Furthermore, all these solutions resolve the problem of missing parental genotype, while offspring with missing genotypes are typically ignored. We propose here an extension to the TDT, called robust TDT (rTDT), able to handle incomplete genotypes on both parents and children and that does not rest on any assumption about the missing data mechanism. rTDT returns minimum and maximum values of TDT that are consistent with all the possible completions of the missing data. We also show that, in some situations, rTDT can achieve both greater power and greater significance than the popular TDT analysis of incomplete data. rTDT is applied to a database of markers of susceptibility to Crohn's disease and it shows that only 2 of the 11 markers originally associated with the phenotype do not depend on assumptions about the missing data mechanism.
Selective Phenotyping for Increased Efficiency in Genetic Mapping Studies
Authors: Jin Chunfang , Lan Hong , Attie Alan D , Churchill Gary A , Bulutuglo Dursun , Yandell Brian S
Published: December 2004

The power of a genetic mapping study depends on the heritability of the trait, the number of individuals included in the analysis, and the genetic dissimilarity among them. In experiments that involve microarrays or other complex physiological assays, phenotyping can be expensive and time-consuming and may impose limits on the sample size. A random selection of individuals may not provide sufficient power to detect linkage until a large sample size is reached. We present an algorithm for selecting a subset of individuals solely on the basis of genotype data that can achieve substantial improvements in sensitivity compared to a random sample of the same size. The selective phenotyping method involves preferentially selecting individuals to maximize their genotypic dissimilarity. Selective phenotyping is most effective when prior knowledge of genetic architecture allows us to focus on specific genetic regions. However, it can also provide modest improvements in efficiency when applied on a whole-genome basis. Importantly, selective phenotyping does not reduce the efficiency of mapping as compared to a random sample in regions that are not considered in the selection process. In contrast to selective genotyping, inferences based solely on a selectively phenotyped population of individuals are representative of the whole population. The substantial improvement introduced by selective phenotyping is particularly useful when phenotyping is difficult or costly and thus limits the sample size in a genetic mapping study.
The cryptochrome (cry) Gene and a Mating Isolation Mechanism in Tephritid Fruit Flies
Authors: An Xin , Tebo Molly , Song Sunmi , Frommer Marianne , Raphael Kathryn A
Published: December 2004

Two sibling species of tephritid fruit fly, Bactrocera tryoni and Bactrocera neohumeralis, are differentiated by their time of mating, which is genetically determined and requires interactions between the endogenous circadian clock and light intensity. The cryptochrome (cry) gene, a light-sensitive component of the circadian clock, was isolated in the two Bactrocera species. The putative amino acid sequence is identical in the two species. In the brain, in situ hybridization showed that cry is expressed in the lateral and dorsal regions of the central brain where PER immunostaining was also observed and in a peripheral cell cluster of the antennal lobes. Levels of cry mRNA were analyzed in whole head, brain, and antennae. In whole head, cry is abundantly and constantly expressed. However, in brain and antennae the transcript cycles in abundance, with higher levels during the day than at night, and cry transcripts are more abundant in the brain and antennae of B. neohumeralis than in that of B. tryoni. Strikingly, these results are duplicated in hybrid lines, generated by rare mating between B. tryoni and B. neohumeralis and then selected on the basis of mating time, suggesting a role for the cry gene in the mating isolation mechanism that differentiates the species.
The L-Type Cyclin CYL-1 and the Heat-Shock-Factor HSF-1 Are Required for Heat-Shock-Induced Protein Expression in Caenorhabditis elegans
Authors: Hajdu-Cronin Yvonne M , Chen Wen J , Sternberg Paul W
Published: December 2004

In a screen for suppressors of activated GOA-1 (Gαo) under the control of the hsp-16.2 heat-shock promoter, we identified three genetic loci that affected heat-shock-induced GOA-1 expression. The cyl-1 mutants are essentially wild type in appearance, while hsf-1 and sup-45 mutants have egg-laying defects. The hsf-1 mutation also causes a temperature-sensitive developmental arrest, and hsf-1 mutants have decreased life span. Western analysis indicated that mutations in all three loci suppressed the activated GOA-1 transgene by decreasing its expression. Heat-shock-induced expression of hsp-16.2 mRNA was reduced in cyl-1 mutants and virtually eliminated in hsf-1 and sup-45 mutants, as compared to wild-type expression. The mutations could also suppress other transgenes under heat-shock control. cyl-1 and sup-45, but not hsf-1, mutations suppressed a defect caused by a transgene not under heat-shock control, suggesting a role in general transcription or a post-transcriptional aspect of gene expression. hsf-1 encodes the C. elegans homolog of the human heat-shock factor HSF1, and cyl-1 encodes a cyclin most similar to cyclin L. We believe HSF-1 acts in heat-shock-inducible transcription and CYL-1 acts more generally in gene expression.
Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate
Authors: Nikoh Naruo , Duty April , Gibson Greg
Published: December 2004

As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal range for Drosophila genes and proteins, and linkage disequilibrium decays rapidly such that haplotype blocks are typically only a few SNPs long. However, intron 1 of 5-HT1A consists of two haplotypes that are at significantly different frequencies in the two populations. Neither this region of the gene nor any of the common amino acid polymorphisms in the three loci associate with either heart rate or heart rate variability. A cluster of SNPs in intron 2 of 5-HT1A, including a triallelic site, do show a highly significant interaction between genotype, sex, and population. While it is likely that a combination of weak, complex selection pressures and population structure has helped shape variation in the serotonin receptors of Drosophila, much larger sampling strategies than are currently adopted in evolutionary genetics will be required to disentangle these effects.
The Population Genetic Theory of Hidden Variation and Genetic Robustness
Authors: Hermisson Joachim , Wagner Günter P
Published: December 2004

One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype.
Direct Estimation of Genetic Principal Components
Authors: Kirkpatrick Mark , Meyer Karin
Published: December 2004

Estimating the genetic and environmental variances for multivariate and function-valued phenotypes poses problems for estimation and interpretation. Even when the phenotype of interest has a large number of dimensions, most variation is typically associated with a small number of principal components (eigen-vectors or eigenfunctions). We propose an approach that directly estimates these leading principal components; these then give estimates for the covariance matrices (or functions). Direct estimation of the principal components reduces the number of parameters to be estimated, uses the data efficiently, and provides the basis for new estimation algorithms. We develop these concepts for both multivariate and function-valued phenotypes and illustrate their application in the restricted maximum-likelihood framework.
Expression Level of sarah, a Homolog of DSCR1, Is Critical for Ovulation and Female Courtship Behavior in Drosophila melanogaster
Authors: Ejima Aki , Tsuda Manabu , Takeo Satomi , Ishii Kunimasa , Matsuo Takashi , Aigaki Toshiro
Published: December 2004

To better understand the genetic bases of postmating responses in Drosophila melanogaster females, we screened a collection of P{GS} insertion lines and identified two insertions in sarah (sra), whose misexpression in the nervous system induced high levels of ovulation in virgins. The gene sra encodes a protein similar to human Down syndrome critical region 1 (DSCR1). The ovulation phenotype was reproduced in transgenic virgins expressing UAS-sra in the nervous system. The flies also extruded the ovipositor toward courting males as seen in wild-type mated females, supporting the notion that ovulation and behavioral patterns are physiologically coupled. The sra insertions were found to be hypomorphic alleles with reduced expression levels. Females homozygous for these alleles show: (1) spontaneous ovulation in virgins, (2) sterility with impaired meiotic progression, and (3) compromised postmating responses with lower ovulation level, higher remating rate, and shorter period for restoration of receptivity. No obvious defects were observed in the homozygous males. The gene sra is predominantly expressed in oocytes, nurse cells, and the nervous system. Taken together, these results indicate that the expression level of sra is critical for ovulation and female courtship behavior, including their postmating changes.
Polyandry, Life-History Trade-Offs and the Evolution of Imprinting at Mendelian Loci
Authors: Mills Walter , Moore Tom
Published: December 2004

Genomic imprinting causes parental origin-dependent differential expression of a small number of genes in mammalian and angiosperm plant embryos, resulting in non-Mendelian inheritance of phenotypic traits. The “conflict” theory of the evolution of imprinting proposes that reduced genetic relatedness of paternally, relative to maternally, derived alleles in offspring of polygamous females supports parental sex-specific selection at gene loci that influence maternal investment. While the theory's physiological predictions are well supported by observation, the requirement of polyandry in the evolution of imprinting from an ancestral Mendelian state has not been comprehensively analyzed. Here, we use diallelic models to examine the influence of various degrees of polyandry on the evolution of both Mendelian and imprinted autosomal gene loci that influence trade-offs between maternal fecundity and offspring viability. We show that, given a plausible assumption on the physiological relationship between maternal fecundity and offspring viability, low levels of polyandry are sufficient to reinforce exclusively the fixation of “greedy” paternally imprinted alleles that increase offspring viability at the expense of maternal fecundity and “thrifty” maternally imprinted alleles of opposite effect. We also show that, for all levels of polyandry, Mendelian alleles at genetic loci that influence the trade-off between maternal fecundity and offspring viability reach an evolutionary stable state, whereas pairs of reciprocally imprinted alleles do not.
Using Temporally Spaced Sequences to Simultaneously Estimate Migration Rates, Mutation Rate and Population Sizes in Measurably Evolving Populations
Authors: Ewing Greg , Nicholls Geoff , Rodrigo Allen
Published: December 2004

We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.
Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes
Authors: Qin Hong , Wu Wei Biao , Comeron Josep M , Kreitman Martin , Li Wen-Hsiung
Published: December 2004

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.