bluuebunny/crossref_metadata_2025 huggingface dataset:
Single crystal galena pillars as highly anisometric dissolution forms
Authors: Bonev Ivan K. , Rice Clive M.
Published: December 2006

Remarkable single crystal galena formations in the unique form of cylindrical or steep conical ‘pillars’ with ‘capitals’ of small rhombododecahedral single crystals of sphalerite, are described. It is suggested that the pillars result from a highly specific process of anisotropic mineral dissolution controlled by a system of internal channels in the original skeletal crystals and represent a kind of dissolution whiskers.
Post-crystallisation modification of the igneous layering in the Nunarssuit and West Kûngnât syenites, South Greenland
Authors: Hodson Mark
Published: December 2006

The chemistry and textures of the minerals in the layered syenites of Nunarssuit and West Kûngnât record a complex post-crystallisation history. The initial cumulus phases were alkali feldspar, pyroxene and olivine, apatite and opaque oxides. Grain size distributions of the pyroxenes and olivines have been modified since crystallisation, possibly during transport of these grains in a density current, prior to deposition in layers. Olivines and pyroxenes re-equilibrated with intercumulus melt. The lower ratio of mafic phases to intercumulus fluid in leucocratic layers has resulted in pyroxene and olivine in these layers undergoing more re-equilibration that in melanocratic layers, consequently pyroxenes and olivines in leucocratic layers are more ferroan. Pyroxenes reacted with either intercumulus or deuteric fluid to form amphibole. In West Kûngnât pyroxene and amphibole re-equilibrated via a later fluid. Olivines reacted with deuteric fluid to produce biotites, probably at temperatures < 550°C. After crystallisation alkali feldspars exsolved, the exsolution textures coarsened in the presence of deuteric fluids with a magmatic origin, possibly at temperatures as low as 450°C. Zoning patterns of apatites and zircons were modified during interactions with either, or both intercumulus or deuteric fluids. Leucocratic layers underwent more modification than melanocratic ones, probably due to the higher concentration of intercumulus melt in the former leading to a higher concentration of deuteric fluids as water exsolved from the magma during cooling. The syenites underwent little compaction during solidification.
Age and petrogenesis of the Qassiarsuk carbonatite-alkaline silicate volcanic complex in the Gardar rift, South Greenland
Authors: Andersen Tom
Published: December 2006

The Qassiarsuk (formerly spelled Qagssiarssuk) complex is located in a roughly E–W trending graben structure between Qassiarsuk village and Tasiusaq settlement in the northern part of the Precambrian Gardar rift, South Greenland. The complex comprises a sequence of alkaline silicate tuffs and extrusive carbonatites interlayered with sandstones, and their subvolcanic equivalents, which represent possible feeders for the extrusive rocks. The Rb-Sr, Sm-Nd and Pb isotopic characteristics of 65 samples of extrusive carbonatite- and silicate tuffs and carbonatite diatremes have been determined by mass spectrometry. The Qassiarsuk complex can be dated to c. 1.2 Ga by Rb-Sr and Pb-Pb isochrons on whole-rocks and mineral separates, agreeing with previous isotopic ages for the volcanic rocks of the Eriksfjord formation in the Eriksfjord area of the Gardar rift, but not with previous, indirect age estimates of >1.31 Ga for assumed Eriksfjord equivalents in the Motzfeldt area further east. Recalculated isotopic compositions at 1.2 Ga indicate that the Qassiarsuk carbonatite- and alkaline-silicate magmas were comagmatic and derived from a depleted mantle source (εNd>4, εSr<−13, time-integrated, single- stage 238U/204Pb ≤ 7.4). The mantle-derived magmas were contaminated with crustal material, equivalent to the local, pre-Gardar granites and gneisses and sediments derived from these. The crustal component has a depleted mantle Nd model age of 2.1-2.6 Ga; at 1.2 Ga it was characterized by εSr = +76, εNd = −8.4, time-integrated, single- stage 238U/204Pb = 8.2−8.3. Strong decoupling of the Pb from the Sr and Nd isotopic systems suggests that the contamination happened only after carbonatitic and alkaline-silicate magmas had evolved from a common parent, by processes such as liquid immisicibility and/or fractional crystallization. Post-magmatic hydrothermal alteration (oxidation, hydration of mafic silicates, carbonatization of melilite) may have contributed further to the contamination of the carbonatite and alkaline silicate rocks of the Qassiarsuk complex.
The origins of carbonatites and related rocks from the Grønnedal-Íka Nepheline Syenite complex, South Greenland: C-O-Sr isotope evidence
Authors: Pearce N. J. G. , Leng M. J. , Emeleus C. H. , Bedford C. M.
Published: December 2006

The Grønnedal-Íka ring complex (1299 ± 17 Ma) in the Gardar province, South Greenland is composed of a range of layered nepheline syenites which were intruded at a late stage by xenolithic syenite and a plug of carbonatite. The complex was subsequently intruded by a variety of basic dykes, including olivine dolerites, kersantites, vogesites, spessartites, camptonites and an alnöite, and then extensively faulted. The nepheline syenite magmas, produced by fractional crystallisation of basic magmas, show a range in δ13C (−3.86 to −7.57‰) and δ18O (8.27 to 15.12‰), distinctly different to the carbonatites which form a tight group with average δ13C = −4.31 + 0.22 ‰, (1 s.d.) and average δ18O = 7.18 ± 0.41‰ (1 s.d.). Initial87Sr/86Sr isotope ratios (typically 0.703) suggest the syenites and carbonatites have not assimilated crustal rocks, and therefore the C and O isotope variation within each group is a result of isotopic evolution during fractional crystallisation. A suite of lamprophyre dykes (δ13C −3.86 to −7.86‰ and δ18O 9.12 to 10.81‰) form a coherent group whose stable isotope compositions overlap part of the syenite field, and again are distinctly different from the carbonatites. A single alnöite has δ13C = −3.32‰ and δ18O = 12.34‰ C and O isotope ratios are consistent with origins of syenitic and lamprophyric magmas from a similar source. Despite geochemical evidence which suggests a genetic link between nepheline syenites and carbonatites, C and O isotopic evidence shows that they are not related directly by liquid immiscibility. Comparisons are made between similar rock types from Grønnedal-Íka and from the Gardar Igaliko Dyke Swarm. The possible role of F in controlling δ13C and δ18O during crystallisation of calcite from carbonatite magmas is discussed.
Neogene–Recent rifting and volcanism in northern Tanzania: relevance for comparisons between the Gardar province and the East African Rift valley
Authors: Dawson J. B.
Published: December 2006

The tectonic position of the intraplate, alkaline volcanic province of N. Tanzania in a broad rift-controlled area astride the boundary between the Tanzania Craton and the circum-cratonic Mozambique Fold Belt, strongly resembles that of the Gardar province of S. Greenland. Earlier-identified petrological analogies between Gardar magmatism and that in the Kenya sector of the East African Rift Valley can be extended to volcanism in N. Tanzania, and analogies specifically with the Gardar agpaitic suite are strengthened by the occurrence of eudialyte and aenigmatite in some Tanzanian peralkaline, silicic volcanics.
Role of CO2 on differentiation of ultramafic alkaline series: liquid immiscibility in carbonate-bearing phonolitic dykes (Polar Siberia)
Authors: Kogarko L. N.
Published: December 2006

The Maimecha-Kotui province in the North of Siberian platform is the largest province of ultramafic alkaline rocks in the world. The province comprises thirty-seven central-type complexes together with numerous dykes. The majority of dykes are radially disposed around the ultramafic alkaline massifs. Data are presented for dykes of the Dolbykha carbonatite complex, which comprises olivine and melilite nephelinites; nosean, calcite and cancrinite phonolites; calcite trachytes and calcite carbonatites.

Some peralkaline phonolitic dykes contain carbonate-bearing globules with sizes of 1−2 mm to 17−20 mm. Globules consist of polycrystalline calcitic aggregates together with albite, phlogopite, apatite, Sr-lueshite, zircon, ancylite, ilmenite and strontianite. The phonolites have phenocrysts of albite, phlogopite and ilmenite. Albite, phlogopite, calcite and nepheline are also present in the groundmass. Analysis of these materials in the light of experimental data on the liquid immiscibility in carbonate-silicate systems suggests that separation of carbonatite from phonolitic melts took place due to immiscibility in the liquid state. I propose that carbonate melts contained originally significantly higher alkali contents which were subsequently lost into the fluid phase due to the incongruent dissolution of calcium-sodium carbonates in aqueous fluid at low temperatures. The discovery of nyerereite in the carbonatite of Polar Siberia confirms this conclusion. I infer that one of the mechanisms for the genesis of carbonatite melt in Polar Siberia was liquid immiscibility in strongly differentiated phonolitic magmas.

The generation of the carbonatites was probably controlled by the depth (and PCO2) of the crustal magma chamber where differentiation took place and probably also by the alkalinity of melts, and the rapidity of magma ascent to the surface.
The Minastira peraluminous granite, Puno, southeastern Peru: a quenched, hypabyssal intrusion recording magma commingling and mixing
Authors: Kontak Daniel J. , Clark Alan H.
Published: December 2006

The Minastira granite, ac.25 Ma subvolcanic plug of fine-grained granitic rock in the Cordillera Oriental of SE Peru, has preserved textures indicative of a history involving mixing of at least two magmas, a volumetrically dominant felsic component and a less voluminous mafic one. The felsic component is represented by variably fractured, altered and embayed crystals of quartz, feldspar, biotite with minor coarsegrained melt- and fluid-inclusion rich apatite, and possible cordierite (now a pseudomorphous Fe-Mg phase), whereas the mafic component is represented by calcic plagioclase. The process of magma mixing is reflected by: (1) ubiquitous sieved-textured plagioclase with complex textural relationships; (2) a large range in plagioclase compositions with reversals and spike patterns in profiles; (3) embayed and internally fractured (thermal shock?) quartz; (4) the rare occurrence of pyroxene coronas on quartz; and (5) textures within biotite suggestive of its incipient breakdown. The lack of mafic enclaves indicates that physico-chemical conditions of the mixing were conducive to homogenization (i.e. chemical diffusion) and a superficially homogeneous rock is now observed. The association of glomeroclasts of crystals originating from both the mafic and felsic end members and a quenched quartz-feldspar matrix indicate that the mixing occurred in an underlying magma chamber.
Characteristics of ore minerals associated with gold at the Prestea mine, Ghana
Authors: Hammond Napoleon Q. , Tabata Hirokazu
Published: December 2006

Gold in Early Proterozoic Birimian greenstone at Prestea in Ghana is associated with base metal sulphides and sulphosalts including arsenopyrite, pyrite, sphalerite, chalcopyrite, pyrrhotite, galena, tetrahedrite, bournonite, boulangerite and jamesonite. The occurrence of the gold is intimately associated with arsenopyrite and the sulphosalts, and to a lesser extent with the other sulphides. The tetrahedrites at Prestea constitute the major component of sulphosalts associated with gold and occurring in two distinct types. Type I show ideal stoichiometric composition. Type II tetrahedrites deviated from the ideal stoichiometry and are represented approximately by the average formula (Cu,Ag)9.61(Fe,Zn)2.39(Sb,As)4S13. The tetrahedrites co-precipitated with gold exhibit ideal characteristics indicating an equilibruim state of the mineralizing fluid during precipitation. Three types of pyrites were distinguished by electron-microprobe analyses based on their As, Co and Ni composition. The As content in type I vary from 0.15 to 0.37 wt%, and contain up to 2 wt.% Co.Type II pyrites are As-rich and form the most dominant with As content ranging from 0.2 to 2.69 wt.%. Ni content varies from below-detection to 1000 ppm. Type III pyrites are poor in the trace elements and consistent with the stoichiometric composition. The mineralization occurred in three paragenetic stages from at least a two-phase hydrothermal fluid, with stage II forming a prolonged and main stage of the ore and gold mineralization. Redox changes in ore fluid which were triggered by episodic pressure releases during fissuring and fracturing caused fluctuation of the activity of the As/Ni ratio and subsequent oscillatory zoning of Ni in As-rich ores.
Minimally differentiated acute myeloid leukemia (FAB AML-M0) is associated with an adverse outcome in children: a report from the Children's Oncology Group, studies CCG-2891 and CCG-2961
Authors: Barbaric Draga , Alonzo Todd A. , Gerbing Robert B. , Meshinchi Soheil , Heerema Nyla A. , Barnard Dorothy R. , Lange Beverly J. , Woods William G. , Arceci Robert J. , Smith Franklin O.
Published: December 2006

To assess the impact of minimally differentiated acute myeloid leukemia (AML-M0) morphology in children, we analyzed 2 sequential Children's Cancer Group AML clinical trials. We compared presenting characteristics and outcomes of 82 CCG-2891 and CCG-2961 patients with de novo, non–Down syndrome (DS) AML-M0 with those of 1620 patients with non-M0 AML, and of 10 CCG-2891 patients with DS-associated AML-M0 with those of 179 with DS-associated non-M0 AML. Morphology and cytogenetics were centrally reviewed. The non-DS AML-M0 children had a lower white blood cell (WBC) count (P = .001) than their non-M0 counterparts and a higher incidence of chromosome 5 deletions (P = .002), nonconstitutional trisomy 21 (P = .027), and hypodiploidy (P = .002). Outcome analyses considering all children with non-DS AML demonstrated no significant differences between M0 and non-M0 patients. Analyses restricted to intensive-timing CCG-2891 and CCG-2961 demonstrated comparable complete response (CR) rates (79% and 78%) between non-DS M0 and non-M0 patients. Overall survival (OS) from diagnosis (38% ± 14% versus 51% ± 3%; P = .160) was not significantly different between the 2 groups. OS from end of induction (45% ± 17% versus 63% ± 3%; P = .038), event-free survival (EFS; 23% ± 11% versus 41% ± 3%; P = .018), and disease-free survival (DFS; 31% ± 14% versus 52% ± 3%; P = .009) were inferior in the M0 group. There was no significant outcome difference between DS-associated AML-M0 and non-M0 children. This study suggests that intensively treated non–DS-associated AML-M0 children have an inferior outcome compared with children with non-M0 AML.
A simple vector system to improve performance and utilisation of recombinant antibodies
Authors: Martin Cecile D , Rojas Gertrudis , Mitchell Joanne N , Vincent Karen J , Wu Jiahua , McCafferty John , Schofield Darren J
Published: December 2006

Background

Isolation of recombinant antibody fragments from antibody libraries is well established using technologies such as phage display. Phage display vectors are ideal for efficient display of antibody fragments on the surface of bacteriophage particles. However, they are often inefficient for expression of soluble antibody fragments, and sub-cloning of selected antibody populations into dedicated soluble antibody fragment expression vectors can enhance expression.

Results

We have developed a simple vector system for expression, dimerisation and detection of recombinant antibody fragments in the form of single chain Fvs (scFvs). Expression is driven by the T7 RNA polymerase promoter in conjunction with the inducible lysogen strain BL21 (DE3). The system is compatible with a simple auto-induction culture system for scFv production. As an alternative to periplasmic expression, expression directly in the cytoplasm of a mutant strain with a more oxidising cytoplasmic environment (Origami 2™ (DE3)) was investigated and found to be inferior to periplasmic expression in BL21 (DE3) cells. The effect on yield and binding activity of fusing scFvs to the N terminus of maltose binding protein (a solubility enhancing partner), bacterial alkaline phosphatase (a naturally dimeric enzymatic reporter molecule), or the addition of a free C-terminal cysteine was determined. Fusion of scFvs to the N-terminus of maltose binding protein increased scFv yield but binding activity of the scFv was compromised. In contrast, fusion to the N-terminus of bacterial alkaline phosphatase led to an improved performance. Alkaline phosphatase provides a convenient tag allowing direct enzymatic detection of scFv fusions within crude extracts without the need for secondary reagents. Alkaline phosphatase also drives dimerisation of the scFv leading to an improvement in performance compared to monovalent constructs. This is illustrated by ELISA, western blot and immunohistochemistry.

Conclusion

Nine scFv expression vectors have been generated and tested. Three vectors showed utility for expression of functional scFv fragments. One vector, pSANG14-3F, produces scFv-alkaline phosphatase fusion molecules which offers a simple, convenient and sensitive way of determining the reactivity of recombinant antibody fragments in a variety of common assay systems.
Herbal medicine: women's views, knowledge and interaction with doctors: a qualitative study
Authors: Vickers Kathryn A , Jolly Kate B , Greenfield Sheila M
Published: December 2006

Background

There is growing concern that serious interactions are occurring between prescribed/over the counter and herbal medicines and that there is a lack of disclosure of herbal use by patients to doctors. This study explores women's perspectives about the safety of herbal remedies, herb-drug interactions and communication with doctors about herbal medicines.

Methods

Qualitative, cross-sectional study, with purposive sampling which took place in Cheshire, UK. Eighteen in depth semi-structured interviews were conducted with female herbal medicine users aged 18 years and above.

Results

The large majority did not inform their GPs of their use of herbal medicines. This was due to lack of physician enquiry, perception of importance and fear of a negative response. Several women were not aware that herbal remedies could interact with prescribed or over the counter medicines. Of the women who had experienced adverse effects none had reported them, believing them of low importance.

Conclusion

The women had little knowledge about herb-drug interactions and rarely disclosed use of herbal medicines to their doctor. Doctors' communication and openness regarding herbal medicines needs to improve and there should be increased access to accurate information on herbal medicines in the public and health care domain.
Assessment of level-walking aperiodicity
Authors: Pecoraro Fabrizio , Mazzà Claudia , Zok Mounir , Cappozzo Aurelio
Published: December 2006

Background:

In gait analysis, walking is assumed to be periodic for the sake of simplicity, despite the fact that, strictly speaking, it can only approximate periodicity and, as such, may be referred to as pseudo-periodic. This study aims at: 1) quantifying gait pseudo-periodicity using information concerning a single stride; 2) investigating the effects of walking pathway length on gait periodicity; 3) investigating separately the periodicity of the upper and lower body parts movement; 4) verifying the validity of foot-floor contact events as markers of the gait cycle period.

Methods:

Ten young healthy subjects (6 males, 23 ± 5 years) were asked to perform various gait trials, first along a 20-m pathway that allowed reaching a steady-state condition, and then along an 8-m pathway. A stereophotogrammetric system was used to reconstruct the 3D position of reflective markers distributed over the subjects' body. Foot contact was detected using an instrumented mat. Three marker clusters were used to represent the movement of the whole body, the upper body (without upper limbs), and the lower body, respectively. Linear and rotational kinetic, and gravitational and elastic potential "energy-like" quantities were used to calculate an index J(t) that described the instantaneous "mechanical state" of the analysed body portion. The variations of J(t) in time allowed for the determination of the walking pseudo-period and for the assessment of gait aperiodicity.

Results:

The suitability of the proposed approach was demonstrated, and it was shown that, for young, healthy adults, a threshold of physiological pseudo-periodicity of walking at natural speed could be set. Higher pseudo-periodicity values were found for the shorter pathway only for the upper body. Irrespective of pathway length, the upper body had a larger divergency from periodicity than the lower body. The error that can be made in estimating the gait cycle duration for the upper body from the heel contacts was shown to be significant.

Conclusion:

The proposed method can be easily implemented in gait laboratories to verify the consistency of a recorded stride with the hypothesis of periodicity.
Concordane of OSTA and lumbar spine BMD by DXA in identifying risk of osteoporosis
Authors: Lu ChunYan , Chen DeCai , Cai YunHua , Wei SongQuan
Published: December 2006

Objective

To investigate the accuracy of Osteoporosis Self-assessment Tool for Asians (OSTA) in identifying the risk of osteoporosis in postmenopausal women. To validate use of OSTA risk index by comparing it with the bone mineral density (BMD) of lumbar spine measured by dual energy X-ray absorptiometry (DXA).

Methods

The data of lumbar spine BMD (LS BMD) measurements by DXA of 218 postmenopausal women of Han nationality in Sichuan province were compared with OSTA risk index. The concordance of OSTA and LS BMD were calculated and analyzed by fourfold table and receiver operating characteristic (ROC) curve.

Results

The prevalence of osteoporosis in these women was 40.4% and 61.5%, with the LS BMD T score cutoffs -2.5 and -2.0, respectively. The sensitivity, specificity, and accuracy of OSTA risk index compared with T score cutoff -2.5 of LS BMD were 59.1%, 56.9% and 57.8%, respectively, while they were 57.5%, 63.1%, 59.6% by T score cutoff -2.0.

Conclusion

For identifying risk of osteoporosis, the concurrence was lower than those reported studies when comparing LS BMD measurements to OSTA risk index in Chinese Han nationality postmenopausal women of Sichuan province. Physicians should identify women who need BMD measurement according to more factors rather than age and body weight.
Sequential allocation and global pattern of movement of the definitive endoderm in the mouse embryo during gastrulation
Authors: Tam Patrick P. L. , Khoo Poh-Lynn , Lewis Samara L. , Bildsoe Heidi , Wong Nicole , Tsang Tania E. , Gad Jacqueline M. , Robb Lorraine
Published: December 2006

During mouse gastrulation, endoderm cells of the dorsal foregut are recruited ahead of the ventral foregut and move to the anterior region of the embryo via different routes. Precursors of the anterior-most part of the foregut and those of the mid- and hind-gut are allocated to the endoderm of the mid-streak-stage embryo, whereas the precursors of the rest of the foregut are recruited at later stages of gastrulation. Loss of Mixl1 function results in reduced recruitment of the definitive endoderm, and causes cells in the endoderm to remain stationary during gastrulation. The observation that the endoderm cells are inherently unable to move despite the expansion of the mesoderm in the Mixl1-null mutant suggests that the movement of the endoderm and the mesoderm is driven independently of one another.
Lipoprotein Lipase mRNA Expression in Whole Blood Is a Prognostic Marker in B Cell Chronic Lymphocytic Leukemia
Authors: Van Bockstaele Femke , Pede Valerie , Janssens Ann , Callewaert Filip , Offner Fritz , Verhasselt Bruno , Philippé Jan
Published: December 2006

Background: Chronic lymphocytic leukemia (CLL) is characterized by high individual variability in clinical course and the need for therapy. Differentiation of prognostic subgroups is based primarily on the mutation status of the genes for the variable region of the immunoglobulin heavy chain (IGHV). The time- and labor-intensive nature of this analysis necessitates the use of easily applicable surrogate markers.

Methods: We developed a quantitative PCR (qPCR) method for determining lipoprotein lipase (LPL) mRNA expression and analyzed samples of lysed whole blood and CD19-selected cells from 50 CLL patients. Associations of LPL and ZAP70 [ζ-chain (TCR) associated protein kinase 70 kDa] expression with IGHV mutation status, overall survival (OS), and treatment-free survival (TFS) were investigated.

Results: Lysed samples of whole blood and CD19-selected cells were similar with respect to LPL expression (R = 0.88; P <0.0001). LPL expression was significantly associated with IGHV mutation status [χ2(1) = 15.3; P <0.0001] and showed an 89.3% specificity, a 68.2% sensitivity, an 83.3% positive predictive value, and a 78.1% negative predictive value for IGHV mutation status. LPL expression was significantly associated with both OS and TFS in log-rank tests (both P values = 0.002). LPL-positive patients had a significantly shorter median TFS time (23 months) than LPL-negative patients (88 months) (P = 0.002).

Conclusions: LPL mRNA expression is a valuable prognostic marker in CLL. The method does not require cell purification, and its applicability with archived samples facilitates its use in the clinical routine and other studies.
Mos1Mutagenesis Reveals a Diversity of Mechanisms Affecting Response ofCaenorhabditis elegansto the Bacterial PathogenMicrobacterium nematophilum
Authors: Yook Karen , Hodgkin Jonathan
Published: December 2006

A specific host–pathogen interaction exists between Caenorhabditis elegans and the gram-positive bacterium Microbacterium nematophilum. This bacterium is able to colonize the rectum of susceptible worms and induces a defensive tail-swelling response in the host. Previous mutant screens have identified multiple loci that affect this interaction. Some of these loci correspond to known genes, but many bus genes [those with a bacterially unswollen (Bus) mutant phenotype] have yet to be cloned. We employed Mos1 transposon mutagenesis as a means of more rapidly cloning bus genes and identifying new mutants with altered pathogen response. This approach revealed new infection-related roles for two well-characterized and much-studied genes, egl-8 and tax-4. It also allowed the cloning of a known bus gene, bus-17, which encodes a predicted galactosyltransferase, and of a new bus gene, bus-19, which encodes a novel, albeit ancient, protein. The results illustrate advantages and disadvantages of Mos1 transposon mutagenesis in this system.
The Impact of Male-Killing Bacteria on Host Evolutionary Processes
Authors: Engelstädter Jan , Hurst Gregory D D
Published: December 2006

Male-killing bacteria are maternally inherited endosymbionts that selectively kill male offspring of their arthropod hosts. Using both analytical techniques and computer simulations, we studied the impact of these bacteria on the population genetics of their hosts. In particular, we derived and corroborated formulas for the fixation probability of mutant alleles, mean times to fixation and fixation or extinction, and heterozygosity for varying male-killer prevalence. Our results demonstrate that infections with male-killing bacteria impede the spread of beneficial alleles, facilitate the spread of deleterious alleles, and reduce genetic variation. The reason for this lies in the strongly reduced fitness of infected females combined with no or very limited gene flow from infected females to uninfected individuals. These two properties of male-killer-infected populations reduce the population size relevant for the initial emergence and spread of mutations. In contrast, use of Wright's equation relating sex ratio to effective population size produces misleading predictions. We discuss the relationship to the similar effect of background selection, the impact of other sex-ratio-distorting endosymbionts, and how our results affect the interpretation of empirical data on genetic variation in male-killer-infected populations.
The Population Biology of Bacterial Plasmids: A Hidden Markov Model Approach
Authors: Ponciano José M , De Gelder Leen , Top Eva M , Joyce Paul
Published: December 2006

Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process using a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.
The SU(VAR)3-9/HP1 Complex Differentially Regulates the Compaction State and Degree of Underreplication of X Chromosome Pericentric Heterochromatin in Drosophila melanogaster
Authors: Demakova Olga V , Pokholkova Galina V , Kolesnikova Tatyana D , Demakov Sergey A , Andreyeva Eugenia N , Belyaeva Elena S , Zhimulev Igor F
Published: December 2006

In polytene chromosomes of Drosophila melanogaster, regions of pericentric heterochromatin coalesce to form a compact chromocenter and are highly underreplicated. Focusing on study of X chromosome heterochromatin, we demonstrate that loss of either SU(VAR)3-9 histone methyltransferase activity or HP1 protein differentially affects the compaction of different pericentric regions. Using a set of inversions breaking X chromosome heterochromatin in the background of the Su(var)3-9 mutations, we show that distal heterochromatin (blocks h26–h29) is the only one within the chromocenter to form a big “puff”-like structure. The “puffed” heterochromatin has not only unique morphology but also very special protein composition as well: (i) it does not bind proteins specific for active chromatin and should therefore be referred to as a pseudopuff and (ii) it strongly associates with heterochromatin-specific proteins SU(VAR)3-7 and SUUR, despite the fact that HP1 and HP2 are depleted particularly from this polytene structure. The pseudopuff completes replication earlier than when it is compacted as heterochromatin, and underreplication of some DNA sequences within the pseudopuff is strongly suppressed. So, we show that pericentric heterochromatin is heterogeneous in its requirement for SU(VAR)3-9 with respect to the establishment of the condensed state, time of replication, and DNA polytenization.
Effects of Introgression and Recombination on Haplotype Structure and Linkage Disequilibrium Surrounding a Locus EncodingBymovirusResistance in Barley
Authors: Stracke Silke , Presterl Thomas , Stein Nils , Perovic Dragan , Ordon Frank , Graner Andreas
Published: December 2006

We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.
Combining Sperm Typing and Linkage Disequilibrium Analyses Reveals Differences in Selective Pressures or Recombination Rates Across Human Populations
Authors: Clark Vanessa J , Ptak Susan E , Tiemann Irene , Qian Yudong , Coop Graham , Stone Anne C , Przeworski Molly , Arnheim Norman , Rienzo Anna Di
Published: December 2006

A previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.
Onset of the DNA Replication Checkpoint in the Early Drosophila Embryo
Authors: Crest Justin , Oxnard Nathan , Ji Jun-Yuan , Schubiger Gerold
Published: December 2006

The Drosophila embryo is a promising model for isolating gene products that coordinate S phase and mitosis. We have reported before that increasing maternal Cyclin B dosage to up to six copies (six cycB) increases Cdk1–Cyclin B (CycB) levels and activity in the embryo, delays nuclear migration at cycle 10, and produces abnormal nuclei at cycle 14. Here we show that the level of CycB in the embryo inversely correlates with the ability to lengthen interphase as the embryo transits from preblastoderm to blastoderm stages and defines the onset of a checkpoint that regulates mitosis when DNA replication is blocked with aphidicolin. A screen for modifiers of the six cycB phenotypes identified 10 new suppressor deficiencies. In addition, heterozygote dRPA2 (a DNA replication gene) mutants suppressed only the abnormal nuclear phenotype at cycle 14. Reduction of dRPA2 also restored interphase duration and checkpoint efficacy to control levels. We propose that lowered dRPA2 levels activate Grp/Chk1 to counteract excess Cdk1–CycB activity and restore interphase duration and the ability to block mitosis in response to aphidicolin. Our results suggest an antagonistic interaction between DNA replication checkpoint activation and Cdk1–CycB activity during the transition from preblastoderm to blastoderm cycles.
Two Events Are Responsible for an Insertion in a Paternally Inherited Mitochondrial Genome of the Mussel Mytilus galloprovincialis
Authors: Burzyński Artur
Published: December 2006

Frequent nonhomologous recombination has been previously postulated to explain the 1045-bp insertion in one mitochondrial sperm-transmitted haplotype of Mytilus galloprovincialis. Such recombination would lead to the disruption of gene order and so the existence of a specific mechanism for maintaining the same gene order in both mitochondrial genomes of Mytilus has been proposed. Here the simpler explanation of the observed structure, involving a tandem duplication and a deletion, is presented. Their occasional occurrence in Mytilus mtDNA proves the similarity, not the difference, between animals with and without DUI.
Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers
Authors: Sekino Masashi , Hara Motoyuki
Published: December 2006

This study presents linkage maps for the Pacific abalone (Haliotis discus hannai) based on 180 microsatellite DNA markers. Linkage mapping was performed using three F1 outbred families, and a composite linkage map for each sex was generated by incorporating map information from the multiple families. A total of 160 markers are placed on the consolidated female map and 167 markers on the male map. The numbers of linkage groups in the composite female and male maps are 19 and 18, respectively; however, by aligning the two maps, 18 linkage groups are formed, which are consistent with the haploid chromosome number of H. discus hannai. The female map spans 888.1 cM (Kosambi) with an average spacing of 6.3 cM; the male map spans 702.4 cM with an average spacing of 4.7 cM. However, we encountered several linkage groups that show a high level of heterogeneity in recombination rate between families even within the same sex, which reduces the precision of the consolidated maps. Nevertheless, we suggest that the composite maps are of significant potential use as a scaffold to further extend the coverage of the H. discus hannai genome with additional markers.
Importance of the Hsp70 ATPase Domain in Yeast Prion Propagation
Authors: Loovers Harriët M , Guinan Emma , Jones Gary W
Published: December 2006

The Saccharomyces cerevisiae non-Mendelian genetic element [PSI+] is the prion form of the translation termination factor Sup35p. The ability of [PSI+] to propagate efficiently has been shown previously to depend upon the action of protein chaperones. In this article we describe a genetic screen that identifies an array of mutants within the two major cytosolic Hsp70 chaperones of yeast, Ssa1p and Ssa2p, which impair the propagation of [PSI+]. All but one of the mutants was located within the ATPase domain of Hsp70, which highlights the important role of regulation of Hsp70–Ssa ATP hydrolysis in prion propagation. A subset of mutants is shown to alter Hsp70 function in a way that is distinct from that of previously characterized Hsp70 mutants that alter [PSI+] propagation and supports the importance of interdomain communication and Hsp70 interaction with nucleotide exchange factors in prion propagation. Analysis of the effects of Hsp70 mutants upon propagation of a second yeast prion [URE3] further classifies these mutants as having general or prion-specific inhibitory properties.
Generating Novel Allelic Variation ThroughActivatorInsertional Mutagenesis in Maize
Authors: Bai Ling , Singh Manjit , Pitt Lauren , Sweeney Meredith , Brutnell Thomas P
Published: December 2006

The maize transposable element Activator (Ac) has been exploited as an insertional mutagen to disrupt, clone, and characterize genes in a number of plant species. To develop an Ac-based mutagenesis platform for maize, a large-scale mutagenesis was conducted targeting the pink scutellum1 locus. We selected 1092 Ac transposition events from a closely linked donor Ac, resulting in the recovery of 17 novel ps1 alleles. Multiple phenotypic classes were identified corresponding to Ac insertions in the 5′-UTR and coding region of the predicted Ps1 gene. To generate a stable allelic series, we employed genetic screens and identified 83 germinally heritable ps1 excision alleles. Molecular characterization of these excision alleles revealed a position-dependent bias in excision allele frequencies and the predominance of 7- and 8-bp footprint products. In total, 19 unique ps1 excision alleles were generated in this study, including several that resulted in weak mutant phenotypes. The analysis of footprint alleles suggests a model of Ac excision in maize that is consistent with recent in vitro studies of hAT element excision. Importantly, the genetic and molecular methods developed in this study can be extended to generate novel allelic variation at any Ac-tagged gene in the genome.
Evaluation of Formalin and Hydrogen Peroxide Treatment Regimes on Rainbow Trout Eyed Eggs
Authors: Barnes Michael E , Soupir Craig A
Published: December 2006

This study examined the use of antifungal chemicals at nonstandard treatment concentrations or treatment intervals during the incubation of eyed eggs of rainbow trout Oncorhynchus mykiss until hatch in vertically stacked incubation trays. Daily chemical treatments of 500, 1,000, and 1,667 mg of commercial formalin (containing 37% formaldehyde)/L for 15 min and a nonchemical, dead-egg-removal control were included in three trials. The second and third trials added a true control (no antifungal measures) and the third trial also incorporated a treatment of formalin at 1,667 mg/L for 15 min every other day. In these three trials, formalin at 1,000 or 1,667 mg/L daily or 1,667 mg/L every other day significantly improved egg survival to hatch relative to the other treatments and completely controlled fungal growth. A fourth trial evaluated treatments of formalin at 750 mg/L for 15 min daily or every other day, hydrogen peroxide at 500 mg/L for 15 min daily or every other day, and control groups for both treatments. Egg survival to hatch was significantly different among the treatments; the daily 750-mg/L formalin treatment produced the greatest number of hatched fry, followed by the treatment with 750 mg/L formalin every other day, the dead-egg-removal control, and daily hydrogen peroxide treatment. Survival in the every-other-day hydrogen peroxide treatment and the true control could only be estimated because of extreme fungal growth, and was substantially less than the other treatments. Only daily 750 mg/L formalin treatments and dead egg removal completely controlled fungal growth. To adequately control fungus and maximize egg survival, either daily 15-min treatments of formalin at concentrations of at least 750 mg/L or every-other-day treatments of formalin at 1,667 mg/L are recommended.
Evaluation of a Fingerling-to-Stocker Phase as Part of a New Production Strategy for the Commercial Farming of Channel Catfish
Authors: D'Abramo Louis R , Steeby James A , Hanson Terrill R , Gerard Patrick D
Published: December 2006

Within a three-phase production strategy for farming channel catfish Ictalurus punctatus, the second phase, fingerling to stocker production, was evaluated. A complementary economic analysis compared the cost of producing stockers, food-size fish net returns, and overall cost of production for a three-phase production system with that of the traditional multiple-batch system. Pond run fingerlings (mean length = 10.7 cm; mean weight = 10 g) were stocked into 0.05-ha experimental earthen ponds at densities of 98,840, 123,550, and 148,260 per hectare. They were fed floating fingerling feed with 36% crude protein to satiation during a 180-d grow-out period. At harvest, mean survival (63.7–72.6%) and mean feed conversion ratio (1.5–1.6) did not differ significantly among treatments. Mean harvested biomass (kg/ha) ranged from 5,766.5 to 9,135.6 and increased as density increased. Mean harvest weight (85.8–94.3 g) decreased as density increased but was not statistically different among treatments. Stocker cost of production was US.17, .18, and .22 per stocker for the highest, medium, and lowest initial fingerling stocking treatments, respectively. For the higher stocking rates, total food-size cost of production (variable and fixed costs) was $1.37/kg, which was .02/kg to .28/kg less than the production costs of food-size catfish in multiple-batch production systems. The mean harvest weight goal of 113.5 g was not achieved in any treatment, but a slightly larger fingerling stocking size combined with seasonal water temperatures should produce the desired weight for stocking into the third phase (final grow out) of production. The estimated production cost for the three-phase system appears to be less than that of the multiple-batch system. In addition, the three-phase system offers other advantages, such as better inventory control and minimal loss from bird depredation. This broad management concept has the flexibility to be modified to meet the needs of individual operations.
Using policy to drive organizational change
Authors: Hornsby Eunice Ellen
Published: December 2006

This chapter addresses recent changes in public policy and organizational practices that affect LGBTQ individuals and the role that organizational policy can play in establishing and maintaining respectful and inclusive workplaces.
Direct adaptive command following and disturbance rejection for minimum phase systems with unknown relative degree
Authors: Hoagg Jesse B. , Bernstein Dennis S.
Published: December 2006

This paper considers parameter‐monotonic direct adaptive command following and disturbance rejection for single‐input single‐output minimum‐phase linear time‐invariant systems with knowledge of the sign of the high‐frequency gain (first non‐zero Markov parameter) and an upper bound on the magnitude of the high‐frequency gain. We assume that the command and disturbance signals are generated by a linear system with known characteristic polynomial. Furthermore, we assume that the command signal is measured, but the disturbance signal is unmeasured. The first part of the paper is devoted to a fixed‐gain analysis of a high‐gain‐stabilizing dynamic compensator for command following and disturbance rejection. The compensator utilizes a Fibonacci series construction to control systems with unknown‐but‐bounded relative degree. We then introduce a parameter‐monotonic adaptive law and guarantee asymptotic command following and disturbance rejection. Copyright © 2006 John Wiley & Sons, Ltd.
Gene frequencies of human platelet alloantigens in Bahraini Arabs
Authors: Al‐Subaie Abeer M. , Al‐Absi Iman K. , Al‐Ola Khadija , Saidi Sarra , Fawaz Naglaa A. , Almawi Wassim Y.
Published: December 2006

Human platelet antigens (HPA) are implicated in the pathophysiology of certain hematological disorders, and as varied distribution of HPA‐1 alleles and genotypes were reported fordifferent countries and ethnic populations, we determined the distribution of HPA‐1, ‐2, ‐3, ‐4, and ‐5 alleles, genotypes and haplotypes for 194 healthy Bahraini subjects by polymerase chain reaction with sequence specific primers. The distribution of the HPA polymorphisms was in Hardy‐Weinberg equilibrium. Allele frequencies of 0.76 and 0.24 (HPA‐1a and ‐1b), 0.77 and 0.23 (HPA‐2a and ‐2b), 0.57 and 0.43 (HPA‐3a and ‐3b), 0.93 and 0.07 (HPA‐4a and ‐4b), and 0.86 and 0.13 (HPA‐5a and ‐5b) were seen. With the exception of HPA‐3a/a (30.4%), the frequencies of homozygous HPA‐1a/a (56.8%), 2a/a (60.1%), 4a/a (87.2%), and 5a/a (75.7%) were higher than those of heterozygous (a/b) or homozygous (b/b) variants. Our results provide basic information for further studies of the HPA system polymorphism, which in turn will be instrumental in understanding and treating immune‐mediated platelet disorders. Am. J. Hematol 2007. © 2006 Wiley‐Liss, Inc.