bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxygen, carbon and strontium isotope study of the carbonatitic dolomite host of the Bayan Obo Fe-Nb-REE deposit, Inner Mongolia, N China
Authors: Le Bas M. J. , Spiro B. , Xueming Yang
Published: December 2006

The large Fe-Nb-REE deposit at Bayan Obo is hosted by a dolomite marble within the thrust complex of marbles, quartzites and slates that belongs to the Bayan Obo Formation of mid-Proterozoic age. The dolomite is either a dolomitized sedimentary limestone subsequently mineralized and tectonically thrust and folded, or a dolomite (or dolomitized) carbonatite intrusion with late-stage recrystallization and mineralization that has been subsequently tectonically deformed.

O and C isotope data indicate that the sedimentary limestones and dolomites of the Bayan Obo Formation, which occur in the thrust stack together with quartzites and slates, have values of δO c. +20 per mil (SMOW) and δC c. zero. In contrast, the coarser grained facies of the large (0.5 × 10 km) dolomite marble which hosts the REE ore body has δO per mil values between +8 and +12 and δC values between −5 and −3, whereas the finer-grained recrystallized and REE-mineralized dolomite marble which occurs close to the ore bodies has δO between +12 to +16 and δC between −4 and zero. 87Sr/86Sr data confirm this distinction: >0.710 for the sedimentary rocks and <0.704 for the coarse- and fine-grained dolomite marbles.

These data are taken to indicate that the large and coarse-grained dolomite was an igneous carbonatite (as borne out by its fenitic contact rocks and trace element geochemistry), and that the finer grained dolomite recrystallized under the influence of mineralizing solutions which entrained groundwater. The stratiform features in the coarse-grained dolomite that are evident in the field are interpreted as tectonic layering.
Oligocene lamproite containing an Al-poor, Ti-rich biotite, Middle Park, northwest Colorado, USA
Authors: Thompson R. N. , Velde D. , Leat P. T. , Morrison M. A. , Mitchell J. G. , Dickin A. P. , Gibson S. A.
Published: December 2006

A small 33 ± 0.8 Ma lamproite pluton is exposed in the midst of a 23–26 Ma basalt-rhyolite province in Middle Park, NW Colorado. It contains abundant phlogopite phenocrysts in a fine-grained groundmass of analcime pseudomorphs after leucite, biotite, potassic richterite, apatite, ilmenite and accessory diopside. The phlogopite phenocryst cores contain ∼4 wt.% TiO2, 1% Cr2O3 and 0.2% BaO. The smallest groundmass biotites have normal pleochroism but compositions unlike any previously reported, with ∼2% Al2O3, ∼8% TiO2 and F <1.5%. Apart from those elements affected by leucite alteration, both the elemental and isotopic composition of this lamproite are close to those of the Leucite Hills, Wyoming. Its Nd-isotopic model age (TDM = 1.6 Ga) is outside the Leucite Hills range but within that of other Tertiary strongly potassic magmatism in the region underlain by the Wyoming craton. Evidence from both teleseismic tomography and the mantle xenoliths within other western USA mafic ultrapotassic igneous suites shows that the total lithospheric thickness beneath NW Colorado was probably ∼150–200 km at 33 Ma, when the Middle Park lamproite was emplaced. This is an important constraint on tectonomagmatic models for the Cenozoic evolution of this northernmost part of the Rio Grande rift system.
Mineral reactions in sulphide systems as indicators of evolving fluid geochemistry – a case study from the Apollo mine, Siegerland, FRG
Authors: Wagner Thomas , Cook Nigel J.
Published: December 2006

The textural and paragenetic relationships of sulphide and sulphosalt minerals within Cu-Pb-Sb-Bi hydrothermal vein mineralization at the Apollo mine, Siegerland, Germany, are interpreted in terms of various reaction sequences. An earlier primary sulphide mineralization hosted within a siderite vein of the Siegerland type, with pyrite, chalcopyrite, sphalerite and galena as main component phases, has been overprinted by Sb-, Bi- and Cu-rich fluids. This superposition resulted in the formation of new quartz-stibnite veins, and various mineral reactions with the primary sulphides including the formation of the sulphosalt minerals semseyite, tetrahedrite, meneghinite, jaskolskiite, boulangerite, bournonite and zinkenite. Based on microprobe analyses of reaction pairs and determination of mineral proportions in some cases, a series of quantitative data for each mineral reaction may be generated. This, in turn, allows for the construction of isocon diagrams permitting the relative mobility and immobility of all chemical elements involved in each reaction to be discussed. Two stages of reactive replacement are identified, characterized by immobile behaviour of S and supply of Sb and Cu during the first stage and relative immobility of S and Sb with no further supply of metals during the second stage. Formation of sulphosalts inside the siderite vein during the first stage is interpreted as a decrease of disequilibrium between hydrothermal fluids and pre-existing vein minerals. Replacement processes of the second stage are interpreted as an equilibration of geochemical contrasts between different points within the siderite vein and also between the siderite and quartz-stibnite vein systems. The geochemical evolution of fluid composition during the entire mineralizing event may therefore be modelled, based on the transfer of chemical components reflected in the succession of mineral reactions. Such an approach has applications to comparable polyphase mineralization sequences, in which an understanding of fluid evolution patterns may greatly assist in the development of genetic models for mineral deposits. Solid-state diffusion and grain-boundary diffusion are considered to be the dominant mechanisms for short-range mass transport, whereas diffusion of ionic and complex species through the fluid is considered to be of major importance in long-range mass transport.
Mineralogical characterization of paulingite from Vinarická Hora, Czech Republic
Authors: Lengauer C. L. , Giester G. , Tillmanns E.
Published: December 2006

A sample of the zeolite paulingite from the locality Vinarická Hora was investigated by means of chemical, thermal, powder and single crystal X-ray methods. The fully transparent, colourless to pale yellow crystals exhibit the form {110} and occur together with phillipsite. The chemical composition is (Ca2.57K2.28Ba1.39Na0.38)(Al11.55Si30.59O84)·27H2O, Z = 16 with minor amounts of Mg (<0.05), Sr (<0.13), Mn (<0.01), and Fe (<0.04). The chemical differences from previously described paulingites are a high Ba-content, a lower Si/(Al+Fe) ratio of 2.64, and a reduced water-content. The calculated density is 2.098 g cm−3, and the observed refractive index is 1.482(2). The dehydration behaviour is characterized by a main weight loss from 24–190°C (−11.2 wt.%, ≅ 21H2O) and a minor weight loss from 190–390°C (−3.1 wt.%, ≅ 6H2O). The rehydration capability was proven up to 150°C. The dehydration process during the main weight loss is accompanied by a reduction of the cell volume of 11%. The refined lattice parameters of the X-ray powder data are a a = 35.1231 (5) Å and a = 33.7485(8) Å of an untreated and a dehydrated sample, respectively. A breakdown of the paulingite structure can be observed while the remaining water content decomposes. The single crystal X-ray refinement of this chemically different sample material derived three main cation positions, which are inside a so called paulingite or π-cage (Ca), between 8-rings of neighbouring π-cages (Ba), and in the centre of the non-planar 8-rings of the γ-cage (K). Further partially occupied cation positions (Ca,Na) were located in the planar 8-rings of the α- and γ-cages. No positions within the double 8-membered rings were detected. The water is localized around the main cation positions and in three clusters of partially occupied sites.
Composition of trioctahedral micas in the Karlovy Vary pluton, Czech Republic and a comparison with those in the Coruubian batholith, SW England
Authors: Stone M. , Klomínský J. , Rajpoot G. S.
Published: December 2006

Trioctahedral micas in the Karlovy Vary pluton range in composition from Fe-biotites in the granites of the Older Intrusive Complex (OIC) through siderophyllite and lithian siderophyllite to zinnwaldite in the granites of the Younger Intrusive Complex (YIC). Li + AlVI + Si would appear to substitute for Fe2+ + AlIV in biotite with a formula similar to that given in Henderson et al. (1989), but Li + Si appears to substitute for Fe2+ + AlIV in the Li-micas. In mica vs. host rock plots, Rb and F show positive linear covariation except for the Li-mica granites, but femic constituents and tFeO/(tFeO + MgO) have separate trends for OIC and YIC granites and micas. Further differences between OIC and YIC granite micas are seen in their Ti and Mg contents and in plots like V vs. SiO2, AlIVvs. Fe/(Fe+Mg) and Li vs. total iron as Fe2+ and in the results of discriminant analysis. These reveal a geochemical hiatus between OIC and YIC granite micas that coincides with a major temporal hiatus.

Biotite compositions in the YIC granites are similar to those in the granites of the Cornubian batholith and reveal a similar magmatic evolution and genesis in which later biotites evolve to lithian siderophyllites with some enrichment in trace alkalis and F. It is suggested that the biotite granites in the YIC were derived from the products of partial fusion of the OIC granites. A less well-marked geochemical hiatus exists between YIC biotites and zinnwaldites. In some plots (e.g. Si vs. Li, Li vs. tFe) apparent continuity between biotite and the Li-micas suggests continuous evolution, but in others (e.g. Rb vs. TiO2, Rb(biotite) vs. Rb(rock)), Li-mica data points stand apart from the biotites suggesting, like the whole rock data, a separate evolution. Comparison with the more abundant data for Li-micas of the Cornubian batholith suggests derivation of the Li-mica granites by partial fusion of the OIC/YIC granite residues.
Jadeite–K-feldspar rocks and jadeitites from northwest Turkey
Authors: Okay Aral I.
Published: December 2006

Blueschist-facies rocks with jadeite-K-feldspar-lawsonite paragenesis occur as exotic blocks in Miocene debris flows in the blueschist belt of northwest Turkey. The jadeite-K-feldspar rocks have a very fine grain size and although recrystallized locally retain a relict porphyritic volcanic texture. The former nepheline microphenocrysts, recognized from their characteristic shapes, are pseudomorphed by jadeite and K-feldspar, while the relict magmatic aegirine has rims of jadeite. The matrix of the rock consists of very fine-grained aggregates of jadeite, K-feldspar and lawsonite. In some blocks, jadeite makes up >60% of the mode. Jadeite, K-feldspar and lawsonite in the blocks are essentially pure end-member in composition. P-T estimates for these rocks are 8 ± 2 kbar and 300 ± 50°C. The preserved volcanic texture, relict aegirine and the bulk rock composition indicate that these rocks represent metamorphosed phonolites. The paragenesis in these rocks shows that jadeite-K-feldspar is a stable mineral pair in blueschist-facies P-T conditions.
Omphacite-diopside vein in an omphacitite block from the Osayama serpentinite melange, Sangun-Renge metamorphic belt, southwestern Japan
Authors: Tsujimori Tatsuki
Published: December 2006

Omphacite (Jd46.1–52.0Ae0–8.4Aug48.0–51.2) and diopside (Jd4.3–6.3Ae0–0.4Aug93.6–95.6) coexist in a vein cutting an omphacitite block in a serpentinite melange of the Oeyama ophiolite, central Chugoku Mountains. The compositional gap between omphacite and diopside is significantly wider than for other omphacitediopside pairs reported in the literature. The intergrowth texture of the omphacite-diopside vein suggests that the clinopyroxene pair was contemporaneously crystallized in the fracture from a Ca-bearing, alkali-rich fluid in a sub-solvus condition. Such a fluid may have been introduced from the surrounding serpentinized clinopyroxene-bearing harzburgite. The stability of omphacite and Al-rich pumpellyite in the matrix and the omphacite-diopside vein indicate that the earlier matrix recrystallization and later fracture filling may have both taken place under high-P-T condition during the melange-forming stage.
Alkali-deficient tourmaline from the Sullivan Pb-Zn-Ag deposit, British Columbia
Authors: Jiang Shao-Yong , Palmer Martin R. , Slack John F.
Published: December 2006

Alkali-deficient tourmalines are found in albitized rocks from the hanging-wall of the Sullivan Pb-Zn-Ag deposit (British Columbia, Canada). They approximate the Mg-equivalent of foitite with an idealized formula □(Mg2Al)Al6Si6O18(BO3)3(OH)4. Major chemical substitutions in the tourmalines are the alkali-defect type [Na*(x) + Mg*(Y) = □(x) + Al(Y)] and the uvite type [Na*(x) + Al(Y) = Ca(x) + Mg*(Y)], where Na* = Na + K, Mg* = Mg + Fe + Mn. The occurrence of these alkali-deficient tourmalines reflects a unique geochemical environment that is either alkali-depleted overall or one in which the alkalis preferentially partitioned into coexisting minerals (e.g. albite).

Some of the alkali-deficient tourmalines have unusually high Mn contents (up to 1.5 wt.% MnO) compared to other Sullivan tourmalines. Manganese has a strong preference for incorporation into coexisting garnet and carbonate at Sullivan, thus many tourmalines in Mn-rich rocks are poor in Mn (<0.2 wt.% MnO). It appears that the dominant controls over the occurrence of Mn-rich tourmalines at Sullivan are the local availability of Mn and the lack of other coexisting minerals that may preferentially incorporate Mn into their structures.
Vitamin K–containing dietary supplements: comparison of synthetic vitamin K1 and natto-derived menaquinone-7
Authors: Schurgers Leon J. , Teunissen Kirsten J. F. , Hamulyák Karly , Knapen Marjo H. J. , Vik Hogne , Vermeer Cees
Published: December 2006

Vitamin K is a cofactor in the production of blood coagulation factors (in the liver), osteocalcin (in bone), and matrix Gla protein (cartilage and vessel wall). Accumulating evidence suggests that for optimal bone and vascular health, relatively high intakes of vitamin K are required. The synthetic short-chain vitamin K1 is commonly used in food supplements, but recently the natural long-chain menaquinone-7 (MK-7) has also become available as an over-the-counter (OTC) supplement. The purpose of this paper was to compare in healthy volunteers the absorption and efficacy of K1 and MK-7. Serum vitamin K species were used as a marker for absorption and osteocalcin carboxylation as a marker for activity. Both K1 and MK-7 were absorbed well, with peak serum concentrations at 4 hours after intake. A major difference between the 2 vitamin K species is the very long half-life time of MK-7, resulting in much more stable serum levels, and accumulation of MK-7 to higher levels (7- to 8-fold) during prolonged intake. MK-7 induced more complete carboxylation of osteocalcin, and hematologists should be aware that preparations supplying 50 μg/d or more of MK-7 may interfere with oral anticoagulant treatment in a clinically relevant way.
Changes in dietary pattern in 15 year old adolescents following a 4 month dietary intervention with school breakfast – a pilot study
Authors: Ask Anne S , Hernes Sigrunn , Aarek Ingebjørg , Johannessen Gaute , Haugen Margaretha
Published: December 2006

Background

Few studies on impact of meals served in school have been published. However, implications of school meals are an actual issue of both public and political concern in several countries. The objective of this study was to evaluate if breakfast served in a lower secondary school could improve dietary habits and school performance among the students.

Methods

All students in 10th grade in a lower secondary school, consisting of two school classes, were invited to participate in a controlled study. The students in one class were offered a free breakfast at the beginning of each school day for 4 months, while the students in the second class were controls. Both classes were educated in the importance of healthy eating, and a data program enabling them to evaluate dietary intake was introduced. The students answered two questionnaires, one on school performance and one short food frequency questionnaire, four weeks before study start and one week after. Body weight and height were measured by the school nurse at the beginning and end of the study. Because of few students in each group, non-parametrical statistic analyses were used.

Results

All students in the intervention group had breakfast at school during the intervention. One week after the intervention the students in the class who received breakfast had returned to their normal breakfast pattern. In the control group the frequency of a lunch intake had increase, as compared to before study start (p < 0.01). An improved food pattern was seen among the male students in the intervention group, as measured by a healthy eating index after the intervention (p < 0.01). Body Mass Index increased statistically significant in both males and females in the control group (p < 0,01 for males and p < 0.05 for females), but not in the intervention group. Improvement in school performance following school breakfast was not found, but the males in the intervention group reported a significant increase in school contentment (p < 0.05).

Conclusion

In a lower secondary school class served breakfast for 4 months, dietary intake changed to a more healthy profile and weight gain was reduced.
Reduced CD4+ subset and Th1 bias of the human iNKT cells in Type 1 diabetes mellitus
Authors: Kis Janos , Engelmann Peter , Farkas Klara , Richman Geoffrey , Eck Shawn , Lolley James , Jalahej Heyam , Borowiec Maciej , Kent Sally C , Treszl Andras , Orban Tihamer
Published: December 2006

Invariant NKT (iNKT) cells are considered to be important in some autoimmune diseases including Type 1 diabetes mellitus (T1DM). So far, the published data are contradictory in regard to the role of iNKT cells in T1DM. We aimed to study iNKT cell frequency and the function of different iNKT cell subgroups in T1DM. We compared the results of four subject groups: healthy (H), long-term T2DM (ltT2DM; more than 1 year), newly diagnosed T1DM (ndT1DM; less than 3 months), and ltT1DM (more than 1 year) individuals. We measured the iNKT cell frequencies by costaining for the invariant TCR α-chain with 6B11-FITC and Vα24-PE. After sorting the Vα24+6B11+ cells, the generated iNKT clones were characterized. We tested CD4, CD8, and CD161 expression and IL-4 and IFN-γ production on TCR stimulation. The CD4+ population among the iNKT cells was decreased significantly in ltT1DM versus ndT1DM, ltT2DM, or H individuals. The T1DM iNKT cell cytokine profile markedly shifted to the Th1 direction. There was no difference in the frequency of iNKT cells in PBMC among the different patient groups. The decrease in the CD4+ population among the iNKT cells and their Th1 shift indicates dysfunction of these potentially important regulatory cells in T1DM.
Transcriptome and phenotypic analysis reveals Gata3-dependent signalling pathways in murine hair follicles
Authors: Kurek Dorota , Garinis George A. , van Doorninck J. Hikke , van der Wees Jacqueline , Grosveld Frank G.
Published: December 2006

The transcription factor Gata3 is crucially involved in epidermis and hair follicle differentiation. Yet, little is known about how Gata3 co-ordinates stem cell lineage determination in skin, what pathways are involved and how Gata3 differentially regulates distinct cell populations within the hair follicle. Here, we describe a conditional Gata3-/- mouse(K14-Gata3-/-) in which Gata3 is specifically deleted in epidermis and hair follicles. K14-Gata3-/- mice show aberrant postnatal growth and development, delayed hair growth and maintenance, abnormal hair follicle organization and irregular pigmentation. After the first hair cycle, the germinative layer surrounding the dermal papilla was not restored; instead, proliferation was pronounced in basal epidermal cells. Transcriptome analysis of laser-dissected K14-Gata3-/- hair follicles revealed mitosis, epithelial differentiation and the Notch, Wnt and BMP signaling pathways to be significantly overrepresented. Elucidation of these pathways at the RNA and protein levels and physiologic endpoints suggests that Gata3 integrates diverse signaling networks to regulate the balance between hair follicle and epidermal cell fates.
Oskar controls morphology of polar granules and nuclear bodies inDrosophila
Authors: Jones Jennifer R. , Macdonald Paul M.
Published: December 2006

Germ cell formation in Drosophila relies on polar granules, which are large ribonucleoprotein complexes found at the posterior end of the embryo. The granules undergo characteristic changes in morphology during development, including the assembly of multiple spherical bodies from smaller precursors. Several polar granule components, both protein and RNA, have been identified. One of these, the protein Oskar, acts to initiate granule formation during oogenesis and to recruit other granule components. To investigate whether Oskar has a continuing role in organization of the granules and control of their morphology, we took advantage of species-specific differences in polar granule structure. The polar granules of D. immigrans fuse into a single large oblong aggregate, as opposed to the multiple, distinct, spherical granules of D. melanogasterembryos. D. immigrans oskar rescues the body patterning and pole cell defects of embryos from D. melanogaster oskar- mothers,and converts the morphology of the polar granules to that of D. immigrans. The nuclear bodies, which are structures that appear to be closely related to polar granules, are also converted to the D. immigrans type morphology. We conclude that oskar plays a persistent and central role in the polar granules, not only initiating their formation but also controlling their organization and morphology.
Intergenomic Epistasis for Fitness: Within-Population Interactions Between Cytoplasmic and Nuclear Genes in Drosophila melanogaster
Authors: Dowling Damian K , Friberg Urban , Hailer Frank , Arnqvist Göran
Published: December 2006

The symbiotic relationship between the mitochondrial and nuclear genomes coordinates metabolic energy production and is fundamental to life among eukaryotes. Consequently, there is potential for strong selection to shape interactions between these two genomes. Substantial research attention has focused on the possibility that within-population sequence polymorphism in mitochondrial DNA (mtDNA) is maintained by mitonuclear fitness interactions. Early theory predicted that selection will often eliminate mitochondrial polymorphisms. However, recent models demonstrate that intergenomic interactions can promote the maintenance of polymorphism, especially if the nuclear genes involved are linked to the X chromosome. Most empirical studies to date that have assessed cytonuclear fitness interactions have studied variation across populations and it is still unclear how general and strong such interactions are within populations. We experimentally tested for cytonuclear interactions within a laboratory population of Drosophila melanogaster using 25 randomly sampled cytoplasmic genomes, expressed in three different haploid nuclear genetic backgrounds, while eliminating confounding effects of intracellular bacteria (e.g., Wolbachia). We found sizable cytonuclear fitness interactions within this population and present limited evidence suggesting that these effects were sex specific. Moreover, the relative fitness of cytonuclear genotypes was environment specific. Sequencing of mtDNA (2752 bp) revealed polymorphism within the population, suggesting that the observed cytoplasmic genetic effects may be mitochondrial in origin.
A Mixed-Model Approach to Association Mapping Using Pedigree Information With an Illustration of Resistance to Phytophthora infestans in Potato
Authors: Malosetti M , van der Linden C G , Vosman B , van Eeuwijk F A
Published: December 2006

Association or linkage disequilibrium (LD)-based mapping strategies are receiving increased attention for the identification of quantitative trait loci (QTL) in plants as an alternative to more traditional, purely linkage-based approaches. An attractive property of association approaches is that they do not require specially designed crosses between inbred parents, but can be applied to collections of genotypes with arbitrary and often unknown relationships between the genotypes. A less obvious additional attractive property is that association approaches offer possibilities for QTL identification in crops with hard to model segregation patterns. The availability of candidate genes and targeted marker systems facilitates association approaches, as will appropriate methods of analysis. We propose an association mapping approach based on mixed models with attention to the incorporation of the relationships between genotypes, whether induced by pedigree, population substructure, or otherwise. Furthermore, we emphasize the need to pay attention to the environmental features of the data as well, i.e., adequate representation of the relations among multiple observations on the same genotypes. We illustrate our modeling approach using 25 years of Dutch national variety list data on late blight resistance in the genetically complex crop of potato. As markers, we used nucleotide binding-site markers, a specific type of marker that targets resistance or resistance-analog genes. To assess the consistency of QTL identified by our mixed-model approach, a second independent data set was analyzed. Two markers were identified that are potentially useful in selection for late blight resistance in potato.
Simulations Provide Support for the Common Disease–Common Variant Hypothesis
Authors: Peng Bo , Kimmel Marek
Published: December 2006

The success of mapping genes involved in complex diseases, using association or linkage disequilibrium methods, depends heavily on the number and frequency of susceptibility alleles of these genes. These methods will be economically and statistically feasible if common diseases are usually influenced by one or a few susceptibility alleles at each locus (common disease–common variant, CDCV, hypothesis), but not so if there is a high degree of allelic heterogeneity. Here, we use forward-time population simulations to investigate the impact of various genetic and demographic factors on the allelic spectra of human diseases, on the basis of two models proposed by Reich and Lander and by Pritchard. Factors considered are more complex demographies, a finite-allele mutation model, population structure and migration, and interaction between disease susceptibility loci. The conclusion is that the CDCV hypothesis holds and that the phenomenon is caused by transient effects of demography (population expansion). As a result, we devise a multilocus generalization of the Reich and Lander model and demonstrate how interaction between loci with respect to their response to selection may lead to complex effects. We discuss the implications for mapping of complex diseases.
Mapping Temporally Varying Quantitative Trait Loci in Time-to-Failure Experiments
Authors: Johannes Frank
Published: December 2006

Existing methods for mapping quantitative trait loci (QTL) in time-to-failure experiments assume that the QTL effect is constant over the course of the study. This assumption may be violated when the gene(s) underlying the QTL are up- or downregulated on a biologically meaningful timescale. In such situations, models that assume a constant effect can fail to detect QTL in a whole-genome scan. To investigate this possibility, we utilize an extension of the Cox model (EC model) within an interval-mapping framework. In its simplest form, this model assumes that the QTL effect changes at some time point t0 and follows a linear function before and after this change point. The approximate time point at which this change occurs is estimated. Using simulated and real data, we compare the mapping performance of the EC model to the Cox proportional hazards (CPH) model, which explicitly assumes a constant effect. The results show that the EC model detects time-dependent QTL, which the CPH model fails to detect. At the same time, the EC model recovers all of the QTL the CPH model detects. We conclude that potentially important QTL may be missed if their time-dependent effects are not accounted for.
Hybrid Mitochondrial Plasmids From Senescence Suppressor Isolates of Neurospora intermedia
Authors: Maas M F P M , Hoekstra Rolf F , Debets Alfons J M
Published: December 2006

We analyzed several natural suppressor isolates of the pKalilo-based fungal senescence syndrome of Neurospora intermedia. The pKalilo plasmid did not increase in titer in these isolates. Nor did it show integration “de novo.” In at least two of the senescence suppressor isolates, pKalilo had formed stable recombinants with other mitochondrial elements. pKalilo/mtDNA recombination junctions were complete and appeared to have been formed via a nonhomologous recombination mechanism. Further analysis revealed that pKalilo had recombined a novel, 2.6-kb cryptic mitochondrial retroplasmid, similar to the mitochondrial retroplasmid pTHR1 from Trichoderma harzianum and retroplasmids of the “Varkud” homology group. The recombinant molecules consisted of pKalilo, the novel element, and short intervening stretches of mtDNA. The latter stretches clearly corresponded to “in vivo” mitochondrial cDNA, suggesting that the molecules had formed via the action of a template-switching reverse transcriptase. We discuss how different types of mitochondrial plasmids interact and how their detrimental effect on the host may be suppressed.
Mutations in SLC45A2 Cause Plumage Color Variation in Chicken and Japanese Quail
Authors: Gunnarsson Ulrika , Hellström Anders R , Tixier-Boichard Michele , Minvielle Francis , Bed'hom Bertrand , Ito Shin'ichi , Jensen Per , Rattink Annemieke , Vereijken Addie , Andersson Leif
Published: December 2006

S*S (Silver), S*N (wild type/gold), and S*AL (sex-linked imperfect albinism) form a series of alleles at the S (Silver) locus on chicken (Gallus gallus) chromosome Z. Similarly, sex-linked imperfect albinism (AL*A) is the bottom recessive allele at the orthologous AL locus in Japanese quail (Coturnix japonica). The solute carrier family 45, member 2, protein (SLC45A2), previously denoted membrane-associated transporter protein (MATP), has an important role in vesicle sorting in the melanocytes. Here we report five SLC45A2 mutations. The 106delT mutation in the chicken S*AL allele results in a frameshift and a premature stop codon and the corresponding mRNA appears to be degraded by nonsense-mediated mRNA decay. A splice-site mutation in the Japanese quail AL*A allele causes in-frame skipping of exon 4. Two independent missense mutations (Tyr277Cys and Leu347Met) were associated with the Silver allele in chicken. The functional significance of the former mutation, associated only with Silver in White Leghorn, is unclear. Ala72Asp was associated with the cinnamon allele (AL*C) in the Japanese quail. The most interesting feature concerning the SLC45A2 variants documented in this study is the specific inhibition of expression of red pheomelanin in Silver chickens. This phenotypic effect cannot be explained on the basis of the current, incomplete, understanding of SLC45A2 function. It is an enigma why recessive null mutations at this locus cause an almost complete absence of both eumelanin and pheomelanin whereas some missense mutations are dominant and cause a specific inhibition of pheomelanin production.
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Authors: Didelot Xavier , Falush Daniel
Published: December 2006

We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/.
The Sensitivity of Yeast Mutants to Oleic Acid Implicates the Peroxisome and Other Processes in Membrane Function
Authors: Lockshon Daniel , Surface Lauren E , Kerr Emily O , Kaeberlein Matt , Kennedy Brian K
Published: December 2006

The peroxisome, sole site of β-oxidation in Saccharomyces cerevisiae, is known to be required for optimal growth in the presence of fatty acid. Screening of the haploid yeast deletion collection identified ∼130 genes, 23 encoding peroxisomal proteins, necessary for normal growth on oleic acid. Oleate slightly enhances growth of wild-type yeast and inhibits growth of all strains identified by the screen. Nonperoxisomal processes, among them chromatin modification by H2AZ, Pol II mediator function, and cell-wall-associated activities, also prevent oleate toxicity. The most oleate-inhibited strains lack Sap190, a putative adaptor for the PP2A-type protein phosphatase Sit4 (which is also required for normal growth on oleate) and Ilm1, a protein of unknown function. Palmitoleate, the other main unsaturated fatty acid of Saccharomyces, fails to inhibit growth of the sap190Δ, sit4Δ, and ilm1Δ strains. Data that suggest that oleate inhibition of the growth of a peroxisomal mutant is due to an increase in plasma membrane porosity are presented. We propose that yeast deficient in peroxisomal and other functions are sensitive to oleate perhaps because of an inability to effectively control the fatty acid composition of membrane phospholipids.
The Effect of Genetic Variation of the Retinoic Acid Receptor-Related Orphan Receptor C Gene on Fatness in Cattle
Authors: Barendse W , Bunch R J , Kijas J W , Thomas M B
Published: December 2006

Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D′ value of linkage disequilibrium was 0.92 although the average r2 was a low 0.18. The RORC:g.3290T>G SNP had the strongest association with marbling. The inferred haplotypes were significantly associated with marbling and the difference between the most divergent haplotypes was 0.35 σp of marbling and 0.28 σp of rump fat, explaining the previously reported QTL effect. cDNA for RORC were sequenced and 2 new alternative transcripts were found. Fetal tissue shows 40 times greater transcription of RORC than adult tissue. The highest expression in fetal tissue was found in liver and kidney, but in adults the longissimus muscle had the greatest expression of the tissues tested.
Mutation of a Ubiquitously Expressed Mouse Transmembrane Protein (Tapt1) Causes Specific Skeletal Homeotic Transformations
Authors: Howell Gareth R , Shindo Mami , Murray Stephen , Gridley Thomas , Wilson Lawriston A , Schimenti John C
Published: December 2006

L5Jcs1 is a perinatal lethal mutation uncovered in a screen for ENU-induced mutations on mouse chromosome 5. L5Jcs1 homozygotes exhibit posterior-to-anterior transformations of the vertebral column midsection, similar to mice deficient for Hoxc8 and Hoxc9. Positional cloning efforts identified a mutation in a novel, evolutionarily conserved, and ubiquitously expressed gene dubbed Tapt1 (Transmembrane anterior posterior transformation 1). TAPT1 is predicted to contain several transmembrane domains, and part of the gene is orthologous to an unusual alternatively spliced human transcript encoding the cytomegalovirus gH receptor. We speculate that TAPT1 is a downstream effector of HOXC8 that may act by transducing or transmitting extracellular information required for axial skeletal patterning during development.
Functional Roles for β1,4-N-Acetlygalactosaminyltransferase-A in Drosophila Larval Neurons and Muscles
Authors: Haines Nicola , Stewart Bryan A
Published: December 2006

Adult Drosophila mutant for the glycosyltransferase β1,4-N-acetlygalactosaminyltransferase-A (β4GalNAcTA) display an abnormal locomotion phenotype, indicating a role for this enzyme, and the glycan structures that it generates, in the neuromuscular system. To investigate the functional role of this enzyme in more detail, we turned to the accessible larval neuromuscular system and report here that larvae mutant for β4GalNAcTA display distinct nerve and muscle phenotypes. Mutant larvae exhibit abnormal backward crawling, reductions in nerve terminal bouton number, decreased spontaneous transmitter-release frequency, and short, wide muscles. This muscle shape change appears to result from hypercontraction since the individual sarcomeres are shorter in mutant muscles. Analysis of muscle calcium signals showed altered calcium handling in the mutant, suggesting a mechanism by which hypercontraction could occur. All of these phenotypes can be rescued by a transgene carrying the β4GalNAcTA genomic region. Tissue-specific expression, using the Gal4-UAS system, reveals that neural expression rescues the mutant crawling phenotype, while muscle expression rescues the muscle defect. Tissue-specific expression did not appear to rescue the decrease in neuromuscular junction bouton number, suggesting that this defect arises from cooperation between nerve and muscle. Altogether, these results suggest that β4GalNAcTA has at least three distinct functional roles.
Neither Maternal nor Zygotic med-1/med-2 Genes Play a Major Role in Specifying the Caenorhabditis elegans Endoderm
Authors: Captan Vasile V , Goszczynski Barbara , McGhee James D
Published: December 2006

The med-1 and med-2 genes encode small, highly similar proteins related to GATA-type transcription factors and have been proposed as necessary for specification of both the mesoderm and the endoderm of Caenorhabditis elegans. However, we have previously presented evidence that neither maternal nor zygotic expression of the med-1/2 genes is necessary to specify the C. elegans endoderm. Contradicting our conclusions, a recent report presented evidence, based on presumed transgene-induced cosuppression, that the med-1/2 genes do indeed show an endoderm-specifying maternal effect. In this article, we reinvestigate med-2(−); med-1(−) embryos using a med-2- specific null allele instead of the chromosomal deficiences used previously and confirm our previous results: the large majority (∼84%) of med-2(−); med-1(−) embryos express gut granules. We also reinvestigate the possibility of a maternal med-1/2 effect by direct injection of med dsRNA into sensitized (med-deficient) hermaphrodites using the standard protocol known to be effective in ablating maternal transcripts, but again find no evidence for any significant maternal med-1/2 effect. We do, however, show that expression of gut granules in med-1/2-deficient embryos is exquisitely sensitive to RNAi against the vacuolar ATPase-encoding unc-32 gene [present on the same multicopy med-1(+)-containing transgenic balancer used in support of the maternal med-1/2 effect]. We thus suggest that the experimental evidence for a maternal med-1/2 effect should be reexamined and may instead reflect cosuppression caused by multiple transgenic unc-32 sequences, not med sequences.
An Analysis of Univalent Segregation in Meiotic Mutants ofArabidopsis thaliana: A Possible Role for Synaptonemal Complex
Authors: Pradillo Mónica , López Eva , Romero Concepción , Sánchez-Morán Eugenio , Cuñado Nieves , Santos Juan L
Published: December 2006

During first meiotic prophase, homologous chromosomes are normally kept together by both crossovers and synaptonemal complexes (SC). In most eukaryotes, the SC disassembles at diplotene, leaving chromosomes joined by chiasmata. The correct co-orientation of bivalents at metaphase I and the reductional segregation at anaphase I are facilitated by chiasmata and sister-chromatid cohesion. In the absence of meiotic reciprocal recombination, homologs are expected to segregate randomly at anaphase I. Here, we have analyzed the segregation of homologous chromosomes at anaphase I in four meiotic mutants of Arabidopsis thaliana, spo11-1-3, dsy1, mpa1, and asy1, which show a high frequency of univalents at diplotene. The segregation pattern of chromosomes 2, 4, and 5 was different in each mutant. Homologous univalents segregated randomly in spo11-1-3, whereas they did not in dsy1 and mpa1. An intermediate situation was observed in asy1. Also, we have found a parallelism between this behavior and the synaptic pattern displayed by each mutant. Thus, whereas spo11-1-3 and asy1 showed low amounts of SC stretches, dsy1 and mpa1 showed full synapsis. These findings suggest that in Arabidopsis there is a system, depending on the SC formation, that would facilitate regular disjunction of homologous univalents to opposite poles at anaphase I.
Telomere Dysfunction Drives Increased Mutation by Error-Prone Polymerases Rev1 and ζ in Saccharomyces cerevisiae
Authors: Meyer Damon H , Bailis Adam M
Published: December 2006

Using a model system, we have shown that replicative senescence is accompanied by a 16-fold increase in base substitution and frameshift mutations near a chromosome end. The increase was dependent on error-prone polymerases required for the mutagenic response to DNA lesions that block the replication fork.
Least Chub Reproduction: Effects of Density, Sex Ratio, and Spawning Substrate Transfer Frequency
Authors: Billman Eric J , Wagner Eric J , Arndt Ronney E
Published: December 2006

The least chub Iotichthys phlegethontis, a small cyprinid endemic to Bonneville Basin, Utah, is at risk of becoming a threatened species in Utah. Captive propagation has become necessary to preserve genetically distinct populations and to produce specimens for reintroduction. We conducted two spawning studies to develop intensive aquaculture techniques for the least chub. In the two studies, 162 adults (78 females) produced a total of 12,492 fry. Adult broodstock density (0.03–0.20 fish/L), male : Female sex ratio (1:1, 1:2, and 2:1), and spawning substrate transfer frequency (one versus two times per week) did not significantly affect production. In the second study, female mortality was significantly different between treatments, as more female mortalities occurred in tanks with one spawning substrate transfer per week than in tanks with two such transfers. Single females paired with single males produced multiple clutches at 2- to 3-week intervals. The relationship between fry production and female body size (g) appeared to be positive and linear between 1.0 and 2.2 g but was unclear for larger fish.
Adult Returns of Volitionally Migrating and Pond-Sedentary Hatchery-Reared Steelhead Smolts
Authors: Tipping Jack M
Published: December 2006

Adult return rates of steelhead Oncorhynchus mykiss that volitionally emigrated as smolts were compared with those of pond-sedentary juveniles forced from a raceway after being allowed 6 weeks of volitional migration opportunity. In 5 years of releases, an average of 7.2% of the smolts remained in the raceway after the volitional migration opportunity. Adult returns of volitional and pond-sedentary fish were statistically similar in all but 1 year of release; in that year, pond-sedentary returns were significantly greater than those from the volitional release. The results suggest that pond-sedentary juvenile steelhead should not be destroyed or placed in nonanadromous waters out of concern for poor adult survival.
Comparative Fatty Acid Composition of Eggs from White Bass Fed Live Food or Commercial Feed
Authors: Lane Ryan L , Kohler Christopher C
Published: December 2006

We evaluated the influence of two broodstock feeding practices on fatty acid composition and viability of eggs in white bass Morone chrysops. The two dietary groups tested were (1) white bass females fed a commercially formulated feed (crude protein, 45%; crude fat, 16%) and (2) white bass females maintained on live food (fathead minnow Pimephales promelas and golden shiners Notemigonus crysoleucas). Significant differences existed between the dietary treatments in egg fatty acid levels. Eggs of white bass fed live food contained more 11-octadecenoic acid (18:1[n-7]), α-linolenic acid (18:3[n-3]), arachidonic acid (20:4[n-6]), docosahexaenoic acid (22:6[n-3]), and total n-3 fatty acids than eggs of fish fed formulated feed. Conversely, eggs of fish fed the formulated feed contained more oleic acid (18:1[n-9]), linoleic acid (18:2[n-6]), and total monoeic acids. Female white bass fed live food produced significantly more viable eggs (68.0 ± 2.0%) at 48 ± 2 h posthatch than did females fed the commercial feed (57.0 ± 2.0% [mean ± SD]). We found that the egg fatty acids of white bass are significantly affected by the diet of the female and suggest that the fatty acid composition of eggs contribute to overall reproductive success and viability of progeny. More information on the nutrient requirements of piscivorous broodstock is needed to allow feeds to be formulated to enhance the viability of eggs and fry.
Cinnamic Acid
Authors: Garbe Dorothea
Published: December 2006

The article contains sections titled:

1.

Introduction

2.

Physical Properties

3.

Chemical Properties

4.

Occurrence in Nature

5.

Production

5.1.

Perkin Reaction

5.2.

Claisen Condensation

5.3.

Benzal Chloride Reaction

5.4.

Oxidation of Cinnamaldehyde

5.5.

Preparation of Cinnamic Acid Esters

6.

Uses

7.

Quality Specifications

8.

Economic Aspects

9.

Toxicology
Saponins
Authors: Schwarz Michael W.
Published: December 2006

The article contains sections titled:

1.Introduction1.1.General Properties1.2.Distribution1.3.Isolation1.4.Structure Elucidation1.5.Analysis2.Pharmacology3.Plant Saponins3.1.Steroid Saponins3.2.Glycoalkaloids3.3.Triterpene Saponins4.Animal Saponins4.1.Asterosaponins4.2.Holothurins
Thiocyanates and Isothiocyanates, Organic
Authors: Romanowski Frank , Klenk Herbert
Published: December 2006

The article contains sections titled:1.Organic Thiocyanates1.1.Introduction1.2.Physical Properties1.3.Chemical Properties1.4.Production1.5.Use and Commercial Names1.6.Toxicology2.Organic Isothiocyanates2.1.Introduction2.2.Physical Properties2.3.Chemical Properties2.4.Production2.5.Quality Specifications and Analysis2.6.Storage and Transport2.7.Commercial Names2.8.Uses2.8.1.Methyl Isothiocyanate2.8.2.Other Organic Isothiocyanates2.9.Toxicology and Industrial Hygiene2.10.Safety Measures and Processing Advice2.11.Ecological Aspects
Xylidines
Authors: Meyer Michael
Published: December 2006

The article contains sections titled:1.Introduction2.Physical Properties3.Chemical Properties4.Industrial Production4.1.Reduction of Nitroxylenes4.2.Amination of Xylenols4.3.Other Processes5.Quality Specifications, Storage, and Transport6.Use6.1.Dye Production6.2.Plant Protection6.3.Production of Pharmaceutical Products, Pharmaceutical Products for Veterinary Medicine, and Vitamins6.4.Other Uses7.Toxicology