bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectrophotometric determination of urinary iodine by the Sandell-Kolthoff reaction subsequent to dry alkaline ashing. Results from the Czech Republic in the period 1994–2002
Authors: Bílek Radovan , Bednář Jiří , Zamrazil Václav
Published: June 2005

The Czech Republic is an iodine-deficient area. Insufficient iodine intake was reduced by enriching cooking salt with iodine in the range 20–34mgI/kg. An important indicator for tracking changes in iodine nutrition over time is accurate information about urinary iodine concentrations in the population. In this paper we describe and characterize our method used for the determination of iodine in biological material, which is based on alkaline ashing of urine specimens preceding Sandell-Kolthoff reaction using brucine as a colorimetric marker. The losses of radioiodine added during sample preparation have not exceeded 0.001%. The detection limit is 2.6μgI/L and the limit of quantification is 11.7μgI/L, with intra-assay precision of 4% and inter-assay precision of 4.9%. During the period 1994–2002, the urinary iodine concentration was determined in 29,612 samples in the Institute of Endocrinology. The mean basal urinary iodine concentrations±SD were 115±69μgI/L. Of the samples, 0.7% were in severe (<20μgI/L), 9.6% in moderate (20–49μgI/L), 40.1% in mild (50–99μgI/L), 35.6% in adequate (100–200μgI/L), and 14.0% in more than adequate (>200μgI/L) subsets of iodine nutrition. A statistically significant (p<0.00001) difference was found between mean male (127μgI/L) and female (112μgI/L) urinary iodine, and an inversely proportional trend also exists in the age-related data.
Comparison of iodine contents in gastric cancer and surrounding normal tissues
Authors: Gulaboglu Mine , Yildiz Leyla , Celebi Fehmi , Gul Mustafa , Peker Kemal
Published: June 2005

It has been suggested that iodine plays an important role in gastric cancer. Gastric cancer ranks first among the cancers in the north-eastern Anatolia region, Turkey, where iodine deficiency is common. In this study, iodine levels were determined in gastric cancer and surrounding normal tissues in 19 patients with gastric cancer. Tissue iodine levels were determined by the Foss method based on the Sandell-Kolt-hoff reaction. Tissue iodine levels were lower in gastric cancer tissue (17.8±3.4ngI/mg protein, mean±SEM) compared with surrounding normal tissue (41.7±8.0ngI/mg protein) (p<0.001). There was positive correlation between the iodine levels in gastric cancer tissue and surrounding normal tissue (r=0.845, p<0.001). There was no significant difference in iodine levels in cancer and surrounding normal tissue between male and female subjects. The iodine deficiency in our region may be one of the factors for increased gastric cancer prevalence. Our results support the hypothesis that iodine plays an important role in gastric cancer development.
Effects of urine dilution on quantity, size and aggregation of calcium oxalate crystals induced in vitro by an oxalate load
Authors: Guerra Angela , Allegri Franca , Meschi Tiziana , Adorni Giuditta , Prati Beatrice , Nouvenne Antonio , Novarini Almerico , Maggiore Umberto , Fiaccadori Enrico , Borghi Loris
Published: June 2005

Increasing urinary volume is an important tool in the prevention of calcium renal stones. However, the mechanism of how it actually works is only partially understood. This study aimed at assessing how urine dilution affects urinary calcium oxalate crystallization. A total of 16 male idiopathic calcium oxalate (CaOx) stone-formers and 12 normal male subjects were studied and 4 h urine samples were taken twice, under low (undiluted urine) and high hydration conditions (diluted urine). An equal oxalate load (1.3mmol/L) was added to both types of urine and the crystallization parameters were assessed. In both stone-formers and normal subjects, the crystallization processes were significantly (p<0.05 or less) more marked in the undiluted urine than in the diluted urine in terms of: a) total quantity of calcium oxalate dihydrate (COD) and calcium oxalate monohydrate (COM) crystals; b) total quantity of crystalline aggregates; and c) aggregation index (i.e., ratio between the area occupied by crystalline aggregates and the area occupied by all the crystals present). The comparison between stone-formers and normal subjects showed that the greatest difference was for the size of COD crystals, which were larger in the urine of the stone-formers. A further important finding was an inverse relationship between changes in urinary volume and in the aggregation index (r=–0.53, p=0.004). In conclusion, urine dilution considerably reduces crystallization phenomena induced in vitro by an oxalate load in both calcium stone-formers and normal subjects.
Circulating levels of nitrated apolipoprotein A-I are increased in type 2 diabetic patients
Authors: Hermo Ricardo , Mier Cristina , Mazzotta Mary , Tsuji Masatomi , Kimura Satoshi , Gugliucci Alejandro
Published: June 2005

Recent work has shown that high-density lipoprotein (HDL) isolated from human atherosclerotic lesions and the blood of patients with established coronary artery disease contains elevated levels of 3-nitrotyrosine and 3-chlorotyrosine. A higher nitrotyrosine content in lipoprotein is significantly associated with diminished cholesterol efflux capacity of the lipoprotein. Since accelerated atherogenesis is a key complication of diabetes mellitus, and nitrosative stress has recently been implicated in diabetic pathology, we set out to demonstrate an increase in the circulating levels of nitrated apolipoprotein A (apoA)-I in type 2 diabetic patients and its putative correlation with metabolic biomarkers. In this work we addressed this hypothesis in a case-control study with 30 type 2 diabetic patients and 30 age-matched control subjects. Nitrated apoA-I was 3280±1910 absorbance peak area/apoA-I (g/L) for diabetic patients and 2320±890 for control subjects (p<0.037). This represents a 50% increase in circulating nitrated apoA-I in diabetic patients to age-matched controls. Diabetic patients also showed increases of a similar magnitude in circulating advanced glycation endproducts measured as pentosidine fluorescence (44.16±16.26 vs. 30.84±12.86 AU; p<0.01) and in circulating lipoperoxides (46.0±18.0 vs. 37.2±18.0nmol/L; p<0.03). No significant correlation was found between nitration of apoA-I and glycosylated hemoglobin or any of the other parameters measured. If proven in subsequent functional and in vivo studies, increased nitrated apoA-I would represent another mechanism by which nitrosative stress participates in diabetic macro-angiopathy.
A simple method for estimating equilibrium constants for serum testosterone binding resulting in an optimal free testosterone index for use in elderly men
Authors: Ross H. Alec , Meuleman Eric J. , Sweep Fred C. G. J.
Published: June 2005

An algorithm was developed to evaluate equilibrium constants for testosterone (Te) and sex hormone-binding globulin (SHBG) or albumin from serum free testosterone (FTe) measurements performed in a panel of 30 healthy elderly men by means of a near-reference method, i.e., symmetric dialysis (affinity constants: SHBG-Te, 1.13×10
Standardized quantification of circulating peripheral tumor cells from lung and breast cancer
Authors: Pachmann Katharina , Clement Joachim H. , Schneider Claus-Peter , Willen Babette , Camara Oumar , Pachmann Ulrich , Höffken Klaus
Published: June 2005

Detection and quantitation of circulating tumor cells from solid epithelial tumors could become a valuable tool for therapy monitoring if the procedure can be standardized. In the present work we assessed the influence of preanalytical handling, storage and white blood cell isolation on analysis of a population of spiked tumor cell-line cells and intrinsically present epithelial cells in the peripheral blood of breast and lung cancer patients and the sensitivity of their detection. Sucrose density separation did not enrich epithelial cells, and even depleted them, leading to a gross underestimation of their numbers (3/13 positive, between 2.9 and 50cells/mL) in comparison to red blood cell lysis (13/13 positive, between 77,200 and 800cells/mL). Short-term storage of whole blood samples for up to 7days had little influence on the number of epithelial cells recovered. The effectiveness of magnetic bead enrichment was dependent on the number of relevant cells and the volume used for enrichment. Red blood cell lysis and fluorochrome-labeled antibody staining in a no-wash procedure with subsequent laser scanning cytometry allowed the detection of circulating epithelial cells in 92% of breast and lung cancer patients. Two examples of how this method can be applied for the longitudinal analysis in individual patients are shown, with an increase in numbers preceding relapse and a decrease paralleling tumor reduction. The proposed simple and easy method allows close monitoring, which may help in real-time analysis of the response of solid tumors, especially their systemic component, to therapy and hopefully will contribute to more individually tailored therapy.
Radioimmunoassay for plasma C-type natriuretic peptide determination: a methodological evaluation
Authors: Del Ry Silvia , Maltinti Maristella , Emdin Michele , Passino Claudio , Catapano Giosué , Giannessi Daniela
Published: June 2005

C-Type natriuretic peptide (CNP) is a member of the family of natriuretic peptides with vasodilatory properties, and is produced and secreted by endothelial cells. It seems to play a central role in the paracrine vasomotor control of tone and to be important in several clinical conditions characterized by endothelial dysfunction. We evaluated the analytical performance of a commercially available radioimmunoassay for CNP after a preliminary extraction with Sep-Pak C18. Its analytical reliability was checked by determination of CNP plasma levels in healthy subjects (n=23) and in patients with different diseases, likely characterized by endothelial dysfunction, such as chronic heart failure (n=133) and cirrhosis (n=84). The extraction yield was 78±3%. Accuracy of the radiommunological determination was evaluated by dilution (45–370μL of extracted plasma) and recovery tests (>80%). Between- and within-assay variabilities were ≤10% and analytical sensitivity was 0.41±0.015pg/tube. Plasma CNP in patients with chronic heart failure and with cirrhosis was significantly raised compared to controls (p<0.0001 and p=0.001, respectively). The sensitivity, accuracy and variability levels of the method proposed for CNP assay was suitable for reliable detection of changes in CNP plasma levels in the clinical setting.
Evaluation of the Konelab 20XT clinical chemistry analyzer
Authors: Stojanović Nataša , Rogić Dunja , Stavljenić-Rukavina Ana
Published: June 2005

The Konelab 20XT (Thermo Electron Oy, Finland) is a clinical chemistry analyzer for colorimetric, immunoturbidimetric and ion-selective electrode measurements. The aim of our work was to evaluate the analytical performances of the Konelab 20XT according to the European Clinical Chemistry Laboratory Standards Guidelines. A total of 30 analytes including substrates, enzymes, electrolytes and specific proteins were tested. Investigation results showed low imprecision (within-run coefficient of variation was below 3.5% and between-day coefficient of variation was less than 2.5% for most analytes at all three levels studied) and acceptable accuracy of the analyzer. No significant sample- or reagent-related carry-over was found. It was demonstrated that the analytical system operates within the claimed linearity ranges. The results compared well with those obtained by instruments routinely used in our laboratory (Olympus AU2700, Behring Nephelometer II). In general, the data on interference by hemoglobin, hyperbilirubinemia and turbidity are in accordance with known facts. However, slight hemolysis was found to interfere with the alkaline phosphatase (ALP) assay and mild lipemia affected the glucose assay. The Konelab 20XT is an easy-to-use analyzer that is suitable for routine and emergency analyses in small laboratories.
Hydrophobisation and densification of wood by different chemical treatments
Authors: Bach Sylvie , Belgacem Mohamed Naceur , Gandini Alessandro
Published: June 2005

Samples of Pinus sylvestris were treated with different reagents bearing isocyanate, carboxylic anhydride or oxirane functions to induce reaction with the OH groups of the various components of wood. Conditions were optimised to achieve maximum grafting. When the reagents also carried a polymerisable function, a monomer (styrene or methyl methacrylate) was incorporated into the wood morphology after the derivatisation reaction. Subsequent radical polymerisation produced chemical incorporation of some of the resulting macromolecules. The properties of the doubly modified samples were assessed using a wide variety of tests. Both the hydrophobic character and the density increased considerably, suggesting improved lifetime and extended domains of application.
Functionalisation of wood by reaction with 3-isocyanatopropyltriethoxysilane: Grafting and hydrolysis of the triethoxysilane end groups
Authors: Tingaut Philippe , Weigenand Oliver , Militz Holger , Jéso Bernard De , Sèbe Gilles
Published: June 2005

The chemical modification of maritime pine sapwood (Pinus pinaster Soland) with 3-isocyanatopropyltriethoxysilane (IPTES) and its subsequent hydrolysis were investigated. The formation of urethane linkages after the carbamoylation reaction was confirmed by Fourier-transform infrared (FTIR) spectroscopy. The weight percent gain (WPG) obtained was found to be commensurate with the quantity of IPTES in the reagent solution. Swelling measurements combined with scanning electron microscopy-energy dispersive X-ray (SEM-EDX) analysis showed that the reaction occurred within the wood cell walls. Hydrolysis of the grafted triethoxysilane ends in highly carbamoylated wood was also envisaged: the modifications generated after prolonged contact with water were studied by FTIR spectroscopy and 13C and 29Si nuclear magnetic resonance cross-polarisation with magic-angle spinning (NMR CP MAS) analysis. The chemical environments found for silicon (Si–OH, Si–OEt or Si–OSi) before and after hydrolysis were thus identified and a schematic representation of the silicon structures most often encountered in modified wood was proposed.
Bioactive phenolic substances in industrially important tree species. Part 4: Identification of two new 7-hydroxy divanillyl butyrolactol lignans in some spruce, fir, and pine species
Authors: Willför Stefan , Eklund Patrik , Sjöholm Rainer , Reunanen Markku , Sillanpää Reijo , Schoultz Sebastian von , Hemming Jarl , Nisula Linda , Holmbom Bjarne
Published: June 2005

A few lignans, that is, 7-hydroxymatairesinol, secoisolariciresinol, lariciresinol, and nortrachelogenin, predominate in a large proportion of the industrially important softwood species used. Some other lignans, of which some still are unidentified, are also present in lower amounts. Softwood knots, i.e., the branch bases inside tree stems, commonly contain exceptionally large amounts of free aglycone lignans, which has provided a great opportunity to isolate sufficient amounts of softwood lignans for structural characterisation. Here we present the identification and characterisation of two new 9-epimers of 7-hydroxy divanillyl butyrolactol lignans, (7S,8R,8′R,9′R)-4,4′,7-trihydroxy-3,3′-dimethoxylignano-9′,9′-lactol and (7S,8R,8′R,9′S)-4,4′,7-trihydroxy-3,3′-dimethoxylignano-9′,9′-lactol, in knotwood of Colorado spruce (Picea pungens), from tentative GC-MS analysis to final determination of the structure by NMR spectroscopy and X-ray analysis. Further analyses have verified the occurrence of these lignans, which were earlier incorrectly addressed by our group as isomers of liovil, in several spruce, pine, and fir species.
Characterization of physiological functions of sapwood IV: Formation and accumulation of lignans in sapwood of Cryptomeria japonica (L.f.) D. Don after felling
Authors: Imai Takanori , Sato Mika , Takaku Naohiro , Kawai Shingo , Ohashi Hideo , Nomura Masaki , Kushi Masayoshi
Published: June 2005

Matairesinol and pinoresinol were isolated from sugisapwood 40 days after felling. These lignans were not detected in the heartwood. Accordingly, they are probably the result of post-mortem biosynthesis in sapwood parenchyma cells.
An assessment of the feasibility of ultrasound as a defect detector in lumber
Authors: Dyk Herman van , Rice Robert W.
Published: June 2005

This study investigated the limitations of certain attributes for use in detecting internal defects using ultrasonic methods in spruce dimension lumber. Wave propagation in the radial direction and the effect of induced defects on ultrasonic wave characteristics were examined. Ultrasonic velocity, a parameter often applied, was found to be ineffective due to changes in wavelength and frequency when large defects were present. Amplitude, peak frequency magnitude and the area under the frequency spectra showed statistically significant differences between clear and defect-bearing samples, but among-sample variation was found to be too high because of localized density differences and microstructure, so that these methods were not consistently reliable. When sound intensity level was calculated, the variation among samples decreased and distinctions could be made between clear and defect-bearing wood, both within and among the samples tested. Certain attributes of the frequency spectra also showed clear changes with the introduction of defects.
Vibrational properties of green wood in high-temperature water vapor
Authors: Kubojima Yoshitaka , Suzuki Youki , Tonosaki Mario
Published: June 2005

The object of this study was to measure basic wood properties when water in wood is lost by heating under high temperature and high humidity. Using Sitka spruce (Picea sitchensis Carr.) specimens with dimensions of 110 mm (R)×25 mm (L)×8 mm (T), temperature and weight were measured and free-free flexural vibration tests were conducted in water vapor at 115–150°C and 75–98% relative humidity. The results were compared to those at high temperatures without humidity control under atmospheric pressure. Early in the drying process, the resonance frequency and loss tangent showed a minimum and maximum, respectively. Temporal changes in the temperature, moisture content and vibrational properties were similar to those in heating without humidity control, while the specific Young's modulus and loss tangent during the drying processes were much smaller and greater, respectively, than those in heating without humidity control. Hence, we concluded that the wood was remarkably softened by high temperature and moisture.
The stiffness modulus in Norway spruce as a function of year ring
Authors: Koponen Tiina , Karppinen Timo , Hæggström Edward , Saranpää Pekka , Serimaa Ritva
Published: June 2005

The elastic properties of Norway spruce were studied by means of ultrasound. Samples were from stems that were grown either at a medium- or a high-fertility site in Finland. The stiffness modulus was determined in the longitudinal, radial, and tangential directions as a function of the distance from the pith using 1-mm-thick samples. Tangentially cut samples contained only earlywood, while radially and longitudinally cut samples contained both earlywood and latewood. The stiffness modulus in the longitudinal direction for Norway spruce grown at a medium-fertility site increased with distance from the pith from 6±1 to 8.5±1 GPa. This parameter increased as the mean microfibril angle decreased. In the radial and tangential directions, the stiffness modulus was nearly constant, at 1±0.15 and 0.35±0.04 GPa, respectively. The longitudinal stiffness modulus of fast-growing clonal trees, which contained a large share of juvenile wood and were growing on a fertile site, was ca. 30% smaller (4±1 GPa near the pith and 6±1 GPa at the age of 12 years) than that of trees on a medium-fertility site. No difference was found in the radial and tangential stiffness modulus between stems grown at the two sites.
Effect of climatic variables on chromated copper arsenate (CCA) leaching during above-ground exposure
Authors: Taylor James L. , Cooper Paul A.
Published: June 2005

Until recently, most research on the leaching of preservatives from treated wood was conducted in the laboratory. Although these studies have contributed to the understanding of leaching, the data generated under controlled conditions often do not apply to leaching during natural exposure and weathering. In addition, little is known about the effects of climatic variables and long-term emission rates. This paper examines leaching of chromated copper arsenate (CCA) from lumber exposed above ground to 685 mm of precipitationduring 351 days of natural weathering. Stepwise multiple regression analysis revealed relationships between leaching and a number of treatment and climatic variables, including: species of wood, initial preservative loading, amount of precipitation, average air temperature, average light intensity, pH and duration of rain event. Regression models explained approximately 30% of the variation in chromium and arsenic leaching and 44% of the variation in copper leaching.
Cis-effects on Meiotic Recombination Across Distinct a1-sh2 Intervals in a Common Zea Genetic BackgroundSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY656756, AY656757, AY656758 and AY662984, AY662985, AY662986, AY662987.
Authors: Yao Hong , Schnable Patrick S
Published: June 2005

Genetic distances across the a1-sh2 interval varied threefold in three near-isogenic stocks that carry structurally distinct teosinte A1 Sh2 haplotypes (from Z. mays spp. mexicana Chalco, Z. mays spp. parviglumis, and Z. luxurians) and a common maize a1::rdt sh2 haplotype. In each haplotype >85% of recombination events resolved in the proximal 10% of the ∼130-kb a1-sh2 interval. Even so, significant differences in the distributions of recombination breakpoints were observed across subintervals among haplotypes. Each of the three previously detected recombination hot spots was detected in at least one of the three teosinte haplotypes and two of these hot spots were not detected in at least one teosinte haplotype. Moreover, novel hot spots were detected in two teosinte haplotypes. Due to the near-isogenic nature of the three stocks, the observed variation in the distribution of recombination events is the consequence of cis-modifications. Although generally negatively correlated with rates of recombination per megabase, levels of sequence polymorphisms do not fully account for the nonrandom distribution of recombination breakpoints. This study also suggests that estimates of linkage disequilibrium must be interpreted with caution when considering whether a gene has been under selection.
Sequence Finishing and Gene Mapping for Candida albicans Chromosome 7 and Syntenic Analysis Against the Saccharomyces cerevisiae GenomeThe entire chromosome 7 sequence has been deposited at DDBJ/EMBL/GenBank under the project accession no. AP006852.
Authors: Chibana Hiroji , Oka Nao , Nakayama Hironobu , Aoyama Toshihiro , Magee B B , Magee P T , Mikami Yuzuru
Published: June 2005

The size of the genome in the opportunistic fungus Candida albicans is 15.6 Mb. Whole-genome shotgun sequencing was carried out at Stanford University where the sequences were assembled into 412 contigs. C. albicans is a diploid basically, and analysis of the sequence is complicated due to repeated sequences and to sequence polymorphism between homologous chromosomes. Chromosome 7 is 1 Mb in size and the best characterized of the 8 chromosomes in C. albicans. We assigned 16 of the contigs, ranging in length from 7309 to 267,590 bp, to chromosome 7 and determined sequences of 16 regions. These regions included four gaps, a misassembled sequence, and two major repeat sequences (MRS) of >16 kb. The length of the continuous sequence attained was 949,626 bp and provided complete coverage of chromosome 7 except for telomeric regions. Sequence analysis was carried out and predicted 404 genes, 11 of which included at least one intron. A 7-kb indel, which might be caused by a retrotransposon, was identified as the largest difference between the homologous chromosomes. Synteny analysis revealed that the degree of synteny between C. albicans and Saccharomyces cerevisiae is too weak to use for completion of the genomic sequence in C. albicans.
Africanization in the United States
Authors: Pinto M Alice , Rubink William L , Patton John C , Coulson Robert N , Johnston J Spencer
Published: June 2005

The expansion of Africanized honeybees from South America to the southwestern United States in <50 years is considered one of the most spectacular biological invasions yet documented. In the American tropics, it has been shown that during their expansion Africanized honeybees have low levels of introgressed alleles from resident European populations. In the United States, it has been speculated, but not shown, that Africanized honeybees would hybridize extensively with European honeybees. Here we report a continuous 11-year study investigating temporal changes in the genetic structure of a feral population from the southern United States undergoing Africanization. Our microsatellite data showed that (1) the process of Africanization involved both maternal and paternal bidirectional gene flow between European and Africanized honeybees and (2) the panmitic European population was replaced by panmitic mixtures of A. m. scutellata and European genes within 5 years after Africanization. The post-Africanization gene pool (1998–2001) was composed of a diverse array of recombinant classes with a substantial European genetic contribution (mean 25–37%). Therefore, the resulting feral honeybee population of south Texas was best viewed as a hybrid swarm.
Genetic Diversity and Genetic Differentiation in Daphnia Metapopulations With Subpopulations of Known Age
Authors: Haag Christoph R , Riek Myriam , Hottinger Jürgen W , Pajunen V Ilmari , Ebert Dieter
Published: June 2005

If colonization of empty habitat patches causes genetic bottlenecks, freshly founded, young populations should be genetically less diverse than older ones that may have experienced successive rounds of immigration. This can be studied in metapopulations with subpopulations of known age. We studied allozyme variation in metapopulations of two species of water fleas (Daphnia) in the skerry archipelago of southern Finland. These populations have been monitored since 1982. Screening 49 populations of D. longispina and 77 populations of D. magna, separated by distances of 1.5–2180 m, we found that local genetic diversity increased with population age whereas pairwise differentiation among pools decreased with population age. These patterns persisted even after controlling for several potentially confounding ecological variables, indicating that extinction and recolonization dynamics decrease local genetic diversity and increase genetic differentiation in these metapopulations by causing genetic bottlenecks during colonization. We suggest that the effect of these bottlenecks may be twofold, namely decreasing genetic diversity by random sampling and leading to population-wide inbreeding. Subsequent immigration then may not only introduce new genetic material, but also lead to the production of noninbred hybrids, selection for which may cause immigrant alleles to increase in frequency, thus leading to increased genetic diversity in older populations.
African Sequence Variation Accounts for Most of the Sequence Polymorphism in Non-AfricanDrosophila melanogaster
Authors: Schöfl Gerhard , Catania Francesco , Nolte Viola , Schlötterer Christian
Published: June 2005

We compared the sequence polymorphism of 12 genomic fragments in six geographically dispersed African populations to one European Drosophila melanogaster population. On the basis of one African and one European population half of these fragments have strongly reduced levels of variability outside of Africa. Despite this striking difference in European variation, we detected no significant difference in African variation between the two fragment classes. The joint analysis of all African populations indicated that all high-frequency European alleles are of African origin. We observed a negative Tajima's D in all African populations, with three populations deviating significantly from neutral equilibrium. Low, but statistically significant, population differentiation was observed among the African populations. Our results imply that the population structure and demographic past of African D. melanogaster populations need to be considered for the inference of footprints of selection in non-African populations.
Patterns of Synonymous Codon Usage in Drosophila melanogaster Genes With Sex-Biased Expression
Authors: Hambuch Tina M , Parsch John
Published: June 2005

The nonrandom use of synonymous codons (codon bias) is a well-established phenomenon in Drosophila. Recent reports suggest that levels of codon bias differ among genes that are differentially expressed between the sexes, with male-expressed genes showing less codon bias than female-expressed genes. To examine the relationship between sex-biased gene expression and level of codon bias on a genomic scale, we surveyed synonymous codon usage in 7276 D. melanogaster genes that were classified as male-, female-, or non-sex-biased in their expression in microarray experiments. We found that male-biased genes have significantly less codon bias than both female- and non-sex-biased genes. This pattern holds for both germline and somatically expressed genes. Furthermore, we find a significantly negative correlation between level of codon bias and degree of sex-biased expression for male-biased genes. In contrast, female-biased genes do not differ from non-sex-biased genes in their level of codon bias and show a significantly positive correlation between codon bias and degree of sex-biased expression. These observations cannot be explained by differences in chromosomal distribution, mutational processes, recombinational environment, gene length, or absolute expression level among genes of the different expression classes. We propose that the observed codon bias differences result from differences in selection at synonymous and/or linked nonsynonymous sites between genes with male- and female-biased expression.
Differential Rates of Local and Global Homogenization in Centromere Satellites From Arabidopsis RelativesSequence data from this article have been deposited with the EMBL/GenBank libraries under accession nos. AY640635, AY640924, AY642784, AY642785, AY642786, AY642787, AY642788, AY642789, AY642790, AY642791, AY642792, AY642793, AY642794, AY642795, AY642796, AY642797, AY642798, AY642799, AY642800, AY642801, AY642802, AY642803, AY642804, AY642805, AY642806, AY656017, AY656018, AY656019, AY656020, AY656021, AY656022, AY656023, AY656024, AY656025, AY656026, AY656027, AY656028, AY656029, and AY792367, AY792498.
Authors: Hall Sarah E , Luo Song , Hall Anne E , Preuss Daphne
Published: June 2005

Higher eukaryotic centromeres contain thousands of satellite repeats organized into tandem arrays. As species diverge, new satellite variants are homogenized within and between chromosomes, yet the processes by which particular sequences are dispersed are poorly understood. Here, we isolated and analyzed centromere satellites in plants separated from Arabidopsis thaliana by 5–20 million years, uncovering more rapid satellite divergence compared to primate α-satellite repeats. We also found that satellites derived from the same genomic locus were more similar to each other than satellites derived from disparate genomic regions, indicating that new sequence alterations were homogenized more efficiently at a local, rather than global, level. Nonetheless, the presence of higher-order satellite arrays, similar to those identified in human centromeres, indicated limits to local homogenization and suggested that sequence polymorphisms may play important functional roles. In two species, we defined more extensive polymorphisms, identifying physically separated and highly distinct satellite types. Taken together, these data show that there is a balance between plant satellite homogenization and the persistence of satellite variants. This balance could ultimately generate sufficient sequence divergence to cause mating incompatibilities between plant species, while maintaining adequate conservation within a species for centromere activity.
Widespread Prevalence of Wolbachia in Laboratory Stocks and the Implications for Drosophila Research
Authors: Clark Michael E , Anderson Cort L , Cande Jessica , Karr Timothy L
Published: June 2005

Wolbachia is an intracellular microbe harbored by a wide variety of arthropods (including Drosophila) and filarial nematodes. Employing several different strategies including male killing, induced parthenogenesis, cytoplasmic incompatibility, and feminization, and acting by as-yet-unknown mechanisms, Wolbachia alters host reproduction to increase its representation within a population. Wolbachia is closely associated with gametic incompatibility but also interacts with Drosophila in other, little understood ways. We report here significant and widespread infection of Wolbachia within laboratory stocks and its real and potential impact on Drosophila research. We describe the results of a survey indicating that ∼30% of stocks currently housed at the Bloomington Drosophila Stock Center are infected with Wolbachia. Cells of both reproductive tissues and numerous somatic organs harbor Wolbachia and display considerable variation in infection levels within and between both tissue types. These results are discussed from the perspective of Wolbachia's potential confounding effects on both host fitness and phenotypic analyses. In addition to this cautionary message, the infection status of stock centers may provide further opportunities to study the genetic basis of host/symbiosis.
A Microsatellite Linkage Map of the European Sea Bass Dicentrarchus labrax L.Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY383721–383728, AY387399–387406, AY430367–430377, AY453615–453617, AY453620–453628, AY523943–523968, AY529493–529497, AY604983–604992, AY628756–628762, AY636156–636161, AY639097–639109, AY639891–639899, AY694149–694154, and AY714324–714334.
Authors: Chistiakov Dimitry A , Hellemans Bart , Haley Chris S , Law Andy S , Tsigenopoulos Costas S , Kotoulas Georgios , Bertotto Daniela , Libertini Angelo , Volckaert Filip A M
Published: June 2005

A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe.
Linkage Mapping of 1454 New Maize Candidate Gene Loci
Authors: Falque Matthieu , Décousset Laurent , Dervins Delphine , Jacob Anne-Marie , Joets Johann , Martinant Jean-Pierre , Raffoux Xavier , Ribière Nicolas , Ridel Céline , Samson Delphine , Charcosset Alain , Murigneux Alain
Published: June 2005

Bioinformatic analyses of maize EST sequences have highlighted large numbers of candidate genes putatively involved in agriculturally important traits. To contribute to ongoing efforts toward mapping of these genes, we used two populations of intermated recombinant inbred lines (IRILs), which allow a higher map resolution than nonintermated RILs. The first panel (IBM), derived from B73 × Mo17, is publicly available from the Maize Genetics Cooperation Stock Center. The second panel (LHRF) was developed from F2 × F252 to map loci monomorphic on IBM. We built framework maps of 237 loci from the IBM panel and 271 loci from the LHRF panel. Both maps were used to place 1454 loci (1056 on map IBM_Gnp2004 and 398 on map LHRF_Gnp2004) that corresponded to 954 cDNA probes previously unmapped. RFLP was mostly used, but PCR-based methods were also performed for some cDNAs to map SNPs. Unlike in usual IRIL-based maps published so far, corrected meiotic centimorgan distances were calculated, taking into account the number of intermating generations undergone by the IRILs. The corrected sizes of our framework maps were 1825 cM for IBM_Gnp2004 and 1862 cM for LHRF_Gnp2004. All loci mapped on LHRF_Gnp2004 were also projected on a consensus map IBMconsensus_Gnp2004. cDNA loci formed clusters near the centromeres except for chromosomes 1 and 8.
Extensivede NovoGenomic Variation in Rice Induced by Introgression From Wild Rice (Zizania latifoliaGriseb.)
Authors: Wang Yong-Ming , Dong Zhen-Ying , Zhang Zhong-Juan , Lin Xiu-Yun , Shen Ye , Zhou Daowei , Liu Bao
Published: June 2005

To study the possible impact of alien introgression on a recipient plant genome, we examined >6000 unbiased genomic loci of three stable rice recombinant inbred lines (RILs) derived from intergeneric hybridization between rice (cv. Matsumae) and a wild relative (Zizania latifolia Griseb.) followed by successive selfing. Results from amplified fragment length polymorphism (AFLP) analysis showed that, whereas the introgressed Zizania DNA comprised <0.1% of the genome content in the RILs, extensive and genome-wide de novo variations occurred in up to 30% of the analyzed loci for all three lines studied. The AFLP-detected changes were validated by DNA gel-blot hybridization and/or sequence analysis of genomic loci corresponding to a subset of the differentiating AFLP fragments. A BLAST analysis revealed that the genomic variations occurred in diverse sequences, including protein-coding genes, transposable elements, and sequences of unknown functions. Pairwise sequence comparison of selected loci between a RIL and its rice parent showed that the variations represented either base substitutions or small insertion/deletions. Genome variations were detected in all 12 rice chromosomes, although their distribution was uneven both among and within chromosomes. Taken together, our results imply that even cryptic alien introgression can be highly mutagenic to a recipient plant genome.
Deep Haplotype Divergence and Long-Range Linkage Disequilibrium at Xp21.1 Provide Evidence That Humans Descend From a Structured Ancestral Population
Authors: Garrigan Daniel , Mobasher Zahra , Kingan Sarah B , Wilder Jason A , Hammer Michael F
Published: June 2005

Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000–160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.
Analysis of the Zebrafish perplexed Mutation Reveals Tissue-Specific Roles for de Novo Pyrimidine Synthesis During Development
Authors: Willer G B , Lee V M , Gregg R G , Link B A
Published: June 2005

The zebrafish perplexed mutation disrupts cell proliferation and differentiation during retinal development. In addition, growth and morphogenesis of the tectum, jaw, and pectoral fins are also affected. Positional cloning was used to identify a mutation in the carbamoyl-phosphate synthetase2-aspartate transcarbamylase-dihydroorotase (cad) gene as possibly causative of the perplexed mutation and this was confirmed by gene knockdown and pyrimidine rescue experiments. CAD is required for de novo biosynthesis of pyrimidines that are required for DNA, RNA, and UDP-dependent protein glycosylation. Developmental studies of several vertebrate species showed high levels of cad expression in tissues where mutant phenotypes were observed. Confocal time-lapse analysis of perplexed retinal cells in vivo showed a near doubling of the cell cycle period length. We also compared the perplexed mutation with mutations that affect either DNA synthesis or UDP-dependent protein glycosylation. Cumulatively, our results suggest an essential role for CAD in facilitating proliferation and differentiation events in a tissue-specific manner during vertebrate development. Both de novo DNA synthesis and UDP-dependent protein glycosylation are important for the perplexed phenotypes.
Association of the GTP-Binding Protein Gtr1p With Rpc19p, a Shared Subunit of RNA Polymerase I and III in Yeast Saccharomyces cerevisiae
Authors: Todaka Yuko , Wang Yonggang , Tashiro Kosuke , Nakashima Nobutaka , Nishimoto Takeharu , Sekiguchi Takeshi
Published: June 2005

Yeast Gtr1p and its human homolog RRAG A belong to the Ras-like small G-protein superfamily and genetically interact with RCC1, a guanine nucleotide exchange factor for Ran GTPase. Little is known regarding the function of Gtr1p. We performed yeast two-hybrid screening using Gtr1p as the bait to find interacting proteins. Rpc19p, a shared subunit of RNA polymerases I and III, associated with Gtr1p. The association of Gtr1p with Rpc19p occurred in a GTP-form-specific manner. RRAG A associated with RPA16 (human Rpc19p homolog) in a GTP-form-specific manner, suggesting that the association is conserved during evolution. Ribosomal RNA and tRNA synthesis were reduced in the gtr1Δ strain expressing the GDP form of Gtr1p, but not the GTP form of Gtr1p. Gel-filtration studies revealed an accumulation of the smaller Rpc19p-containing complex, but not of A135, in the gtr1Δ strain. Here, we propose that Gtr1p is involved in RNA polymerase I and III assembly by its association with Rpc19p and could be a mediator that links growth regulatory signals with ribosome biogenesis.
The Fission Yeast Schizosaccharomyces pombe Has Two Importin-α Proteins, Imp1p and Cut15p, Which Have Common and Unique Functions in Nucleocytoplasmic Transport and Cell Cycle Progression
Authors: Umeda Makoto , Izaddoost Shahed , Cushman Ian , Moore Mary Shannon , Sazer Shelley
Published: June 2005

The nuclear import of classical nuclear localization signal-containing proteins depends on importin-α transport receptors. In budding yeast there is a single importin-α gene and in higher eukaryotes there are multiple importin-α-like genes, but in fission yeast there are two: the previously characterized cut15 and the more recently identified imp1. Like other importin-α family members, Imp1p supports nuclear protein import in vitro. In contrast to cut15, imp1 is not essential for viability, but imp1Δ mutant cells exhibit a telophase delay and mild temperature-sensitive lethality. Differences in the cellular functions that depend on Imp1p and Cut15p indicate that they each have unique physiological roles. They also have common roles because the imp1Δ and the cut15-85 temperature-sensitive mutations are synthetically lethal; overexpression of cut15 partially suppresses the temperature sensitivity, but not the mitotic delay in imp1Δ cells; and overexpression of imp1 partially suppresses the mitotic defect in cut15-85 cells but not the loss of viability. Both Imp1p and Cut15p are required for the efficient nuclear import of both an SV40 nuclear localization signal-containing reporter protein and the Pap1p component of the stress response MAP kinase pathway. Imp1p and Cut15p are essential for efficient nuclear protein import in S. pombe.
A Genomic Screen for Yeast Vacuolar Membrane ATPase Mutants
Authors: Sambade Maria , Alba Mercedes , Smardon Anne M , West Robert W , Kane Patricia M
Published: June 2005

V-ATPases acidify multiple organelles, and yeast mutants lacking V-ATPase activity exhibit a distinctive set of growth defects. To better understand the requirements for organelle acidification and the basis of these growth phenotypes, ∼4700 yeast deletion mutants were screened for growth defects at pH 7.5 in 60 mm CaCl2. In addition to 13 of 16 mutants lacking known V-ATPase subunits or assembly factors, 50 additional mutants were identified. Sixteen of these also grew poorly in nonfermentable carbon sources, like the known V-ATPase mutants, and were analyzed further. The cwh36Δ mutant exhibited the strongest phenotype; this mutation proved to disrupt a previously uncharacterized V-ATPase subunit. A small subset of the mutations implicated in vacuolar protein sorting, vps34Δ, vps15Δ, vps45Δ, and vps16Δ, caused both Vma− growth phenotypes and lower V-ATPase activity in isolated vacuoles, as did the shp1Δ mutation, implicated in both protein sorting and regulation of the Glc7p protein phosphatase. These proteins may regulate V-ATPase targeting and/or activity. Eight mutants showed a Vma− growth phenotype but no apparent defect in vacuolar acidification. Like V-ATPase-deficient mutants, most of these mutants rely on calcineurin for growth, particularly at high pH. A requirement for constitutive calcineurin activation may be the predominant physiological basis of the Vma− growth phenotype.
The mei-P26 Gene Encodes a RING Finger B-box Coiled-Coil-NHL Protein That Regulates Seizure Susceptibility in Drosophilia
Authors: Glasscock Edward , Singhania Ayush , Tanouye Mark A
Published: June 2005

Seizure-suppressor mutations provide unique insight into the genes and mechanisms involved in regulating nervous system excitability. Drosophila bang-sensitive (BS) mutants present a useful tool for identifying seizure suppressors since they are a well-characterized epilepsy model. Here we describe the isolation and characterization of a new Drosophila seizure-suppressor mutant that results from disruption of the meiotic gene mei-P26, which belongs to the RBCC-NHL family of proteins. The mei-P26 mutation reduces seizures in easily shocked (eas) and slamdance (sda) epileptic flies following mechanical stimulation and electroconvulsive shock. In addition, mutant mei-P26 flies exhibit seizure thresholds at least threefold greater than those of wild type. The mei-P26 phenotypes appear to result from missense mutation of a critical residue in the NHL protein-protein interaction domain of the protein. These results reveal a surprising role for mei-P26 outside of the germline as a regulator of seizure susceptibility, possibly by affecting synaptic development as a ubiquitin ligase.