bluuebunny/crossref_metadata_2025 huggingface dataset:
Autosomal dominant polycystic kidney disease: Prenatal diagnosis by DNA analysis and sonography at 14 weeks
Authors: Ceccherini I. , Lituania M. , Cordone M. S. , Perfumo F. , Gusmano R. , Callea F. , Archidiacono N. , Romeo G.
Published: March 2007

A pregnant woman affected with autosomal dominant polycystic kidney disease (ADPKD) had a history of an affected fetus, diagnosed by sonography at 29 weeks of pregnancy. The proband's father was also affected. DNA analysis performed on chorionic villi at 11 weeks during a second pregnancy predicted an affected fetus, and sonographic examination at 14 weeks confirmed the diagnosis.
Missed prenatal diagnosis of fragile‐X syndrome
Authors: Webb T. P. , Bundey S. , McKinley Mark
Published: March 2007

An account is given of a pregnancy in an obligatory carrier of the fragile‐X syndrome, in whom examination of chorionic villus cells and fetal blood cells showed the presence of a male fetus who lacked the fragile‐X chromosome. However, at 3 months of age he had 14 per cent of fragile‐X cells in his blood. Reasons are suggested for this error in diagnosis. The empirical risk for an error of this sort is 3 per cent.
Prenatal diagnosis of Opitz (BBB) syndrome in the second trimester by ultrasound detection of hypospadias and hypertelorism
Authors: Hogdall C. , Siegel‐Bartelt J. , Toi A. , Ritchie S.
Published: March 2007

Prenatal diagnosis in a kindred with the Opitz (BBB) syndrome is presented. The inheritance is consistent with either autosomal dominant inheritance with sex limited expression or X‐linked inheritance. The abnormalities in the kindred consist of hypertelorism, hypospadias, ambiguous genitalia, urocolic fistula, imperforate anus, mental retardation, diaphragmatic hernia, and malrotation with volvulus. A male fetus at 19 weeks was found by ultrasound to have hypertelorism and hypospadias with a small phallus consistent with the syndrome. The diagnosis was confirmed by pathologic examination after pregnancy termination. This is the first report of prenatal diagnosis of Opitz syndrome by ultrasonographic demonstration of hypertelorism and hypospadias in the second trimester.
Familial marker chromosome due to 3:1 Disjunction of t(9;15) in a grandparent
Authors: Winsor Elizabeth J. T. , van Allen Margot I.
Published: March 2007

An extra small chromosome detected in amniotic fluid was identified as the product of a translocation [46,XX,t(9;15)(p24;q11.2)]. This case is unusual in that individuals with the unbalanced karyotype resulting from a 3:1 disjunction are phenotypically normal.
Prenatal analysis of insulin receptor autophosphorylation in a family with leprechaunism
Authors: Maassen J. A. , Lindhout D. , Reuss A. , Kleijer W. J.
Published: March 2007

We describe a method for the isolation and functional characterization of insulin receptors from chorionic villi and cultured amniotic fluid cells. The functionality of these receptors is assayed by measuring the insulin‐induced stimulation of autophosphorylation of the receptor β‐chain. The method is expected to allow the prenatal diagnosis of those forms of lep‐rechaunism and related diseases which are the result of a decreased stimulation by insulin of receptor autophosphorylation. A pregnancy at risk for leprechaunism was examined and an unaffected child was correctly predicted by study of the functionality of the insulin receptor on cultured amniocytes and by echoscopic examination.
First‐trimester prenatal diagnosis of the nijmegen breakage syndrome and ataxia telangiectasia using an assay of radioresistant dna synthesis
Authors: Jaspers Nicolaas G. J. , van der Kraan Magna , Linssen Peter C. M. L. , Maçek Milan , Seemanová Eva , Kleijer Wim J.
Published: March 2007

Prenatal diagnosis was performed in two pregnancies at risk of the Nijmegen breakage syndrome. In one pregnancy, an affected fetus was diagnosed by demonstration of radioresistant DNA synthesis, using autoradiographic detection of incorporated tritiated thymidine in cultured chorionic villus cells. The diagnosis was confirmed in fetal skin fibroblasts. In the other case, the fetus appeared unaffected.

Using the same procedure, unaffected fetuses were predicted from chorionic villus cells in two pregnancies at risk of ataxia telangiectasia, which is another genetic disorder showing the feature of radioresistant DNA synthesis.

The present biochemical method for prenatal detection of Nijmegen breakage syndrome and ataxia telangiectasia can be used as a simplified alternative to the cytogenetic procedures reported earlier for ataxia telangiectasia.
Prenatal diagnosis of a double bisatellited marker with an unusual copy number ratio
Authors: Waters J. J. , Ferguson‐Smith M. E. , Carter N. , Alexander J. L. , Hodgson S. V.
Published: March 2007

Prenatal diagnosis, by amniocentesis, revealed mosaicism with respect to a bisatellited, apparently dicentric, DA/DAPI positive, de novo marker. The following cell lines were observed in decreasing order of frequency: 46,XX > 48.XX, + mar, + mar » 47,XX, + mar. The pregnancy was terminated and post‐mortem examination revealed an apparently normal fetus. Cytogenetic studies of fetal and placental tissues revealed approximately the same level of mosaicism together with the unusual copy number ratio seen in the amniotic fluid cultures. Non‐disjunction at the first post‐zygotic mitotic division giving rise to a mosaic: 46,XX/ 48,XX, + mar, + mar followed by subsequent mitotic instability of the marker could account for the unusual copy number ratio.
Prenatal diagnosis of citrullinaemia: Review of a 10‐year experience including recent use of DNA analysis
Authors: Northrup Hope , Beaudet Arthur L. , O'Brien William E.
Published: March 2007

Prenatal diagnosis of citrullinaemia has been accomplished by three different methods to date: (1) enzyme assay of cultured fetal cells; (2) quantification of citrullirie in amniotic fluid supernatant; and (3) incorporation of [14C]citrulline into protein by cultured fetal cells. Our laboratory has used these methods to perform prenatal diagnosis for 28 fetuses over a 10‐year period. More recently, DNA polymorphisms were used for prenatal diagnosis by linkage analysis. Of the 28 fetuses studied, 23 were predicted to be unaffected, four were predicted to be affected, and results were conflicting in one case where [14C]citrulline incorporation erroneously indicated an affected fetus but linkage analysis correctly predicted an unaffected fetus. Because of low levels of enzyme activity in heterozygotes and in certain amniotic fluid cell types, biochemical diagnosis of citrullinaemia is complicated by the risk of false affected results, although [14C]citrulline incorporation is relatively reliable. When informative, linkage analysis is the preferable method for cases with a 25 per cent risk. The risk of false affected results makes prenatal diagnosis for cases with less than 25 per cent risk of questionable value.
Trisomy 12 mosaicism detected by mid–trimester amniocentesis
Authors: Petrella Rena , Hirschhorn Kurt
Published: March 2007

Trisomy 12 mosaicism was found in about 15 per cent of cultured amniocytes obtained from a 32‐year‐old white female at 17·6 weeks of gestation. Termination of pregnancy was elected and multiple tissues were obtained for chromosome analysis. Of 158 cells examined, only 1 cell in placenta was found with an extra number 12 chromosome. Pathological examination of the fetus did not reveal significant physical abnormalities. This report illustrates the difficulty of confirming trisomy 12 mosaicism which has been detected on prenatal diagnosis. The presence of trisomy 12 in one placental cell obtained from the curettage specimen suggests the possibility of confined placental mosaicism in this case.
Resolution of DNA linkage discrepancies through analysis of a VNTR locus in a family study of cystic fibrosis
Authors: Cahill T. C. , Bookstein R. , Axelrod F. , Ngo K.‐Y. , Scioscia A. L.
Published: March 2007

First‐trimester prenatal diagnosis of a fetus at 25 per cent risk for cystic fibrosis (CF) was performed by indirect linkage analysis of polymorphic markers using Southern blotting and polymerase chain reaction (PCR) amplification. The results revealed discrepancies in the allelic patterns between the father and the affected child, thereby complicating the prediction of fetal outcome. Analysis of a highly polymorphic VNTR locus within the human retinoblas‐toma (RB) gene on chromosome 13 showed that the affected child and the fetus did not have the same biological father, and therefore the affected child could not be used to determine linkage of markers in the father of the fetus. The analysis of VNTR loci can be an effective method of resolving conflicting data during prenatal diagnosis of monogenic diseases.
Ultrasonographic method for detection of haemoglobin Bart's hydrops fetalis in the second trimester of pregnancy
Authors: Kanokpongsakdi S. , Fucharoen S. , Vatanasiri C. , Thonglairoam V. , Winichagoon P. , Manassakorn J.
Published: March 2007

In nine pregnant women at risk for fetal alpha‐thalassaemia, the two affected fetuses were diagnosed by ultrasonography at 18–20 weeks' gestation. In countries with limited resources, ultrasonography provides a cost‐effective method of prenatal screening for this condition.
Imaging of Cell/Substrate Contacts on Polymers by Total Internal Reflection Fluorescence Microscopy
Authors: Burmeister J. S. , Truskey G. A. , Yarbrough J. L. , Reichert W. M.
Published: March 2007

A simplified model of total internal reflection fluorescence (TIRF) emission of fluorescently labeled cell membranes [Reichert, W. M.; Truskey, G. A. J. Cell Sci. 1990, 96, 219–230] was used to determine the topography of the cell membrane in apposition to a polymer‐coated surface. The homopolymer substrates weie spun cast films of hydrophilic poly (hydroxy ethyl methaciylate) (polyHEMA) or hydrophobic poly(ethyl methacrylate) (polyEMA). Bovine aortic endothelial cells (BAEC) on preadsorbed fibronectin polymer substrates were either plated for 24 h, fixed, labeled, and examined by TIRF microscopy (TIRFM) and phase‐contrast microscopy or plated for 2 h and tested for their adhesion strength in a parallel‐plate flow chamber. BAEC attached to polyHEMA showed no evidence of focal contact formation. However, BAEC attached to polyEMA were well spread and showed an array of focal contacts. TIRFM data were transformed to construct a detailed topographical mapof relative cell/substrate separation distances. Virtually all of the BAEC plated to polyHEMA were sheared from the surface when subjected to a 50 dyn/cm2 burst of laminar flow, whereas only 10% of the BAEC were sheared from the polyEMA surface. These data suggest that the polyHEMA and polyEMA surface properties (e.g., hydrophobicity) correlate with the presence of BAEC focal contacts and the BAEC attachment strength.
A Simplified Model for the Disruption of Escherichia colṙ. The Effect of Cell Septation
Authors: Middelberg Anton P. J. , O'Neill Brian K. , Thomas Connor J.
Published: March 2007

A new model for the disruption of Escherichia coli by high‐pressure homogenization has been previously presented. Initial model development assumed a bimodal distribution of effective cell strengths to allow for a possible difference in strength between septated and nonseptated cells. A considerably simpler model is obtained when any difference in strength is neglected and a normal distribution is employed. In this article, the disruption of a culture with an abnormally high septated fraction is examined. Disruption versus pressure curves are predicted using both the bimodal and normal approximations to the strength distribution. An examination of disrupted cultures by optical and electron microscopy suggests that septated cells are indeed weaker, thus implying that a bimodal approximation is strictly correct. However, comparison of the model predictions with the experimental results suggests that the simple normal distribution provides sufficient predictive accuracy even for cultures with a high septated fraction.
Geochemistry, geology, and isotopic (Sr, S, and B) composition of evaporites in the Lake St. Martin impact structure: New constraints on the age of melt rock formation
Authors: Leybourne Matthew I. , Denison Rodger E. , Cousens Brian L. , Bezys Ruth K. , Gregoire D. Conrad , Boyle Dan R. , Dobrzanski Ed
Published: March 2007

We report new Sr, S, and B isotopic data for evaporites (gypsum, anhydrite), carbonates, melt rocks, gneisses, and groundwaters recovered in and around the Lake St. Martin (LSM) impact structure, Interlake Region, Manitoba, Canada. The LSM meteorite impacted Devonian to Ordovician carbonates and sandstones of the eastern Williston Basin, resulting in partial melting of underlying Superior Province (∼2.5 Ga) gneisses of the Canadian Shield. Overlying the LSM melt rocks are red beds and evaporites (anhydrite/gypsum/glauberite) previously inferred to have been deposited during the Jurassic. The 87Sr/86Sr (lowest values cluster at 0.70836) and δ34SCDT (+23.7 ± 0.9‰) of the evaporites, combined with B isotope compositions of associated groundwaters (δ11BNBS951 = +25 to +28‰), are consistent with evaporite deposition within the impact structure near the edge of an ocean‐connected salina. The establishment of a marine origin for the evaporites offers a method of age assignment using the secular variation of S and Sr isotopes in seawater. Comparison of Sr and S isotope results with the seawater curves precludes Jurassic deposition for the evaporites or correlation with Watrous and Amaranth formation evaporites, previously considered correlative with those at LSM. The lowest Sr and mean of S isotope values from the LSM evaporites are similar to seawater in the latest Devonian, consistent with conodonts recovered from carbonate breccia overlying melt rocks, and we suggest this as an alternative age of the evaporites. Data presented here preclude a Jurassic age for the evaporites and therefore for the impact event.
Evolution of North Atlantic ERA40 tropical cyclone representation
Authors: Manning Danielle M. , Hart Robert E.
Published: March 2007

The evolving representation of Atlantic tropical cyclones (TCs) in the ERA40 reanalysis dataset from 1957 through 2001 is analyzed using metrics of intensity and the three‐dimensional cyclone phase space. On average, TC structural representation within the ERA40 has shifted two Saffir‐Simpson (SS) categories over the 45 years. Thus, a category three TC during 1957–1971 is comparable in ERA40 representation to a category one during 1988–2001. Further, the ERA40 does not statistically distinguish between category three and four hurricanes within any given tercile. It is also found that less than seven millibars of ERA40 MSLP separate a category one from a five TC, mean ERA40 MSLP does not always decrease with increasing SS category, and not all SS categories are statistically significant with regard to MSLP. It follows that great caution should be exercised when using ERA40 to diagnose long‐term trends in TC structure and intensity within the Atlantic.
Role of the Bering Strait in the thermohaline circulation and abrupt climate change
Authors: Hu Aixue , Meehl Gerald A. , Han Weiqing
Published: March 2007

Here we investigate the role of the Bering Strait (BS) in the thermohaline circulation (THC) response to added freshwater forcing (hosing) in the subpolar North Atlantic, through analyzing simulations of a fully coupled climate model with an open and closed BS. Results show that the THC declines similarly with an open and closed BS during hosing. However, the recovery of the THC is delayed by about a century in the closed BS simulation than in the open BS one after the hosing is off. The closed BS prevents the added freshwater being transported from the Atlantic into the Pacific via the Arctic as in the open BS case. Further, the freshwater supply is elevated significantly after the hosing by exporting the freshwater stored in the Arctic during hosing, as sea ice, back to the North Atlantic. This stabilizes the surface stratification there and suppresses the recovery of the deep convection.
On the relationship between the Indian summer monsoon and river flow in the Aral Sea basin
Authors: Schiemann Reinhard , Glazirina Mariya G. , Schär Christoph
Published: March 2007

We study the contemporaneous relationship between the intensity of the Indian Summer Monsoon (ISM) and runoff in the major rivers of the Aral Sea basin (Amudarya, Syrdarya) and some of their subcatchments. To this end, we use All‐India rainfall (AIR) data, CRU surface observations of precipitation and temperature, ERA40 atmospheric data, and natural discharge data corrected for human interference. We show that there is a highly significant positive correlation between ISM intensity and Amudarya runoff. This finding cannot be explained by the spill‐over of ISM precipitation over the Hindu Kush into the Amudarya basin. Instead, we suggest that the observed co‐variability is mediated by tropospheric temperature variations due to fluctuations in the ISM intensity. These variations are known to be due to Rossby‐wave propagation in response to condensational heating during monsoon precipitation. We hypothesise that the corresponding anomalies in surface temperatures imply anomalies in meltwater formation.
Backscattering enhancement on spheroid‐shaped hydrometeors: Considerations in water and ice particles of uniform size and Marshall‐Palmer distributed rains
Authors: Kobayashi Satoru , Oguchi Tomohiro , Tanelli Simone , Im Eastwood
Published: March 2007

A second‐order scattering theory is derived for uniformly oriented spheroidal hydrometeors with a general drop size distribution in a single layer. Effects of backscattering enhancement are evaluated for a nadir pointing radar with a finite beam width at millimeter wave frequencies. Spheroids of uniform size are first studied to characterize the deviations from the spherical theories. For water spheroids, the difference between the cross term (backscattering enhancement term) and the ladder term (conventional multiscattering term) becomes larger as the spheroids deviate from the spherical shape. On the contrary, for ice spheroids, this difference is negligible. Marshall‐Palmer distributed rains with Pruppacher‐Pitter‐form drops are studied using the spheroidal approximation. The results confirm the validity of the spherical approximation used in the preceding works within the accuracy limit of measurement. In the Marshall‐Palmer distributed rains, the second‐order scattering effect becomes serious as the footprint radius increases. Hence the second‐order scattering is to be taken into account for accurate measurement of hydrometeor reflectivity for a spaceborne radar because of its large footprint radius.
Energy Levels and Observed Spectral Lines of Krypton, Kr I through Kr XXXVI
Authors: Saloman E. B.
Published: March 2007

The energy levels and observed spectral lines of the krypton atom, in all stages of ionization for which experimental data are available, have been compiled. Sufficient data were found to generate level and line tables for Kr I–Kr X and Kr XVIII–Kr XXXVI. For Kr XXXV and Kr XXXVI and most of Kr XXXIV theoretical values are compiled for the energy levels. In all of the other stages a few lines, some of which may be only tentative classifications, are reported. In addition for Kr I, separate tables of energy levels are tabulated for the isotopes Kr86 and Kr84. Experimental g factors are included for Kr I and Kr II. A value, either experimental, semiempirical, or theoretical, is included for the ionization energy of each ion.
Permittivity of Pure Water, at Standard Atmospheric Pressure, over the Frequency Range –25THz and the Temperature Range –100°C
Authors: Ellison W. J.
Published: March 2007

All the currently available experimental permittivity data for pure water are used to derive an interpolation function that precisely represents ε(ν,t,) at standard atmospheric pressure, for frequencies and temperatures in the ranges 0⩽ν⩽25THz and 0⩽t⩽100°C. The permittivity data is represented in terms of relaxations and resonances processes. There are three relaxations in the microwave region and two resonances in the far infrared. The temperature dependence of the relaxation and resonance parameters are determined. For example, at 25°C the three relaxation frequencies are 18.56GHz, 167.83GHz, 1.944THz and the two resonance frequencies are 4.03 and 14.48THz.
QSPR Modeling of Partition Coefficients and Henry’s Law Constants for 75 Chloronaphthalene Congeners by Means of Six Chemometric Approaches—A Comparative Study
Authors: Puzyn Tomasz , Falandysz Jerzy
Published: March 2007

n -octanol/water and n-octanol/air partition coefficients were calculated for 75 chloronaphthalenes (CNs) by means of quantitative structure-property relationship (QSPR) strategy to fill significant lacks in the empirical data. The QSPR models based on quantum-chemical descriptors computed on the level of density functional theory using B3LYP functional and 6-311++G** basis set. For each property, six models were identified using chemometric approaches such as: multiple regression method, principal component regression, partial least square regression, partial least square regression with initial elimination of the uninformative variables, partial least square regression with variable selection by a genetic algorithm (GA-PLS), and neural networks with variable selection by a genetic algorithm (GA-NN). They were calibrated and validated using the experimentally measured values of logKOW available for 16 congeners and the values of logKOA existing for 43 congeners. The models were compared regarding to their complexity and prediction ability. For best predictive model logKOW values of 75 CNs varied from 3.93 to 6.68, while that of logKOA, from 5.93 to 11.64. Root mean square errors of prediction for the best (GA-NN) models were 0.065 and 0.091, respectively. Further, values of logKAW and KH of CNs were calculated based on predicted logKOW and logKOA data. Depending on the CN congener logKAW varied from −1.68 to −5.21 and that of KH from 0.02 to 51.24. The errors of partitioning data computed in this study were of the same order of magnitude as reported for experimentally derived partitioning data, which confirmed applicability of the proposed modeling scheme for successful determination of logKOW and KOA. Accordingly, a new procedure of the computational partitioning data generation based on partial least square regression with variable selection by a genetic algorithm (GA-PLS) and neural networks with variable selection by a genetic algorithm (GA-NN) was optimized and proposed for future use.
Developmental and adult phenotyping directly from mutant embryonic stem cells
Authors: George Sophia H. L. , Gertsenstein Marina , Vintersten Kristina , Korets-Smith Ella , Murphy John , Stevens Mary E. , Haigh Jody J. , Nagy Andras
Published: March 2007

Tetraploid embryo complementation assay has shown that mouse ES cells alone are capable of supporting embryonic development and adult life of mice. Newly established F
1
hybrid ES cells allow the production of ES cell-derived animals at a high enough efficiency to directly make ES cell-based genetics feasible. Here we report the establishment and characterization of 12 new F
1
hybrid ES cell lines and the use of one of the best (G4) in a gain- and loss-of-function genetic study, where the
in vivo
phenotypes were assessed directly from ES cell-derived embryos. We found the generation of G4 ES cell-derived animals to be very efficient. Furthermore, even after two consecutive rounds of genetic modifications, the majority of transgenic lines retained the original potential of the parental lines; with 10–40% of chimeras producing ES cell-derived animals/embryos. Using these genetically altered ES cells, this success rate, in most cases, permitted the derivation of a sufficient number of mutants for initial phenotypic analyses only a few weeks after the establishment of the cell lines. Although the experimental design has to take into account a moderate level of uncontrolled damage on ES cell lines, our proof-of-principle experiment provides useful data to assist future designs harnessing the power of this technology to accelerate our understanding of gene function.
Competition for antigen determines the stability of T cell–dendritic cell interactions during clonal expansion
Authors: Garcia Zacarias , Pradelli Emmanuelle , Celli Susanna , Beuneu Hélène , Simon Aurélie , Bousso Philippe
Published: March 2007

The regulation of T cell–dendritic cell (DC) contacts during clonal expansion is poorly defined. Although optimal CD4 T cell responses require prolonged exposure to antigen (Ag), it is believed that stable T cell–DC interactions occur only during the first day of the activation process. Here we show that recently activated CD4 T cells are in fact fully competent for establishing contact with Ag-bearing DC. Using two-photon imaging, we found that whereas prolonged interactions between activated T cells and Ag-bearing DCs were infrequent at high T cell precursor frequency, they were readily observed for a period of at least 2 days when lower numbers of T cells were used. We provide evidence that, when present in high numbers, Ag-specific T cells still gained access to the DC surface but were competing for the limited number of sites on DCs with sufficient peptide–MHC complexes for the establishment of a long-lived interaction. Consistent with these findings, we showed that restoration of peptide–MHC level on DCs at late time points was sufficient to recover interactions between activated T cells and DCs. Thus, the period during which CD4 T cells continue to establish stable interactions with DCs is longer than previously thought, and its duration is dictated by both Ag levels and T cell numbers, providing a feedback mechanism for the termination of CD4 T cell responses.
A pure population of lung alveolar epithelial type II cells derived from human embryonic stem cells
Authors: Wang Dachun , Haviland David L. , Burns Alan R. , Zsigmond Eva , Wetsel Rick A.
Published: March 2007

Alveolar epithelial type II (ATII) cells are small, cuboidal cells that constitute ≈60% of the pulmonary alveolar epithelium. These cells are crucial for repair of the injured alveolus by differentiating into alveolar epithelial type I cells. ATII cells derived from human ES (hES) cells are a promising source of cells that could be used therapeutically to treat distal lung diseases. We have developed a reliable transfection and culture procedure, which facilitates, via genetic selection, the differentiation of hES cells into an essentially pure (>99%) population of ATII cells (hES-ATII). Purity, as well as biological features and morphological characteristics of normal ATII cells, was demonstrated for the hES-ATII cells, including lamellar body formation, expression of surfactant proteins A, B, and C, α-1-antitrypsin, and the cystic fibrosis transmembrane conductance receptor, as well as the synthesis and secretion of complement proteins C3 and C5. Collectively, these data document the successful generation of a pure population of ATII cells derived from hES cells, providing a practical source of ATII cells to explore in disease models their potential in the regeneration and repair of the injured alveolus and in the therapeutic treatment of genetic diseases affecting the lung.
Dopamine D1 receptors regulate protein synthesis-dependent long-term recognition memory via extracellular signal-regulated kinase 1/2 in the prefrontal cortex
Authors: Nagai Taku , Takuma Kazuhiro , Kamei Hiroyuki , Ito Yukio , Nakamichi Noritaka , Ibi Daisuke , Nakanishi Yutaka , Murai Masaaki , Mizoguchi Hiroyuki , Nabeshima Toshitaka , Yamada Kiyofumi
Published: March 2007

Several lines of evidence suggest that extracellular signal-regulated kinase1/2 (ERK1/2) and dopaminergic system is involved in learning and memory. However, it remains to be determined if the dopaminergic system and ERK1/2 pathway contribute to cognitive function in the prefrontal cortex (PFC). The amount of phosphorylated ERK1/2 was increased in the PFC immediately after exposure to novel objects in the training session of the novel object recognition test. An inhibitor of ERK kinase impaired long-term recognition memory 24 h after the training although short-term memory tested 1 h after the training was not affected by the treatment. The dopamine D1 receptor agonist increased ERK1/2 phosphorylation in the PFC in vivo as well as in cortical neurons in vitro. Microinjection of the dopamine D1 receptor antagonist into the PFC impaired long-term recognition memory whereas the D2 receptor antagonist had no effect. Immunohistochemistry revealed that exposure to novel objects resulted in an increase in c-Fos expression in the PFC. Microinjection of the protein synthesis inhibitor anisomycin into the PFC impaired the long-term recognition memory. These results suggest that the activation of ERK1/2 following the stimulation of dopamine D1 receptors is necessary for the protein synthesis-dependent long-term retention of recognition memory in the PFC.
Theredox imbalancedMutants of Arabidopsis Differentiate Signaling Pathways for Redox Regulation of Chloroplast Antioxidant Enzymes
Authors: Heiber Isabelle , Ströher Elke , Raatz Bodo , Busse Ingo , Kahmann Uwe , Bevan Mike W. , Dietz Karl-Josef , Baier Margarete
Published: March 2007

A network of enzymatic and nonenzymatic antioxidants protects chloroplasts from photooxidative damage. With all enzymatic components being nuclear encoded, the control of the antioxidant capacity depends on chloroplast-to-nucleus redox signaling. Using an Arabidopsis (Arabidopsis thaliana) reporter gene line expressing luciferase under control of the redox-sensitive 2-cysteine peroxiredoxin A (2CPA) promoter, six mutants with low 2CPA promoter activity were isolated, of which five mutants show limitations in redox-box regulation of the 2CPA promoter. In addition to 2CPA, the transcript levels for other chloroplast antioxidant enzymes were decreased, although a higher oxidation status of the ascorbate pool, a higher reduction state of the plastoquinone pool, and an increased oxidation status of the 2-Cys peroxiredoxin pool demonstrated photooxidative stress conditions. Greening of the mutants, chloroplast ultrastructure, steady-state photosynthesis, and the responses to the stress hormone abscisic acid were wild type like. In the rosette state, the mutants were more sensitive to low CO2 and to hydrogen peroxide. Comparison of gene expression patterns and stress sensitivity characterizes the mutants as redox imbalanced in the regulation of nuclear-encoded chloroplast antioxidant enzymes and differentiates redox signaling cascades.
Regulation of NH4
+ Transport by Essential Cross Talk between AMT Monomers through the Carboxyl Tails
Authors: Neuhäuser Benjamin , Dynowski Marek , Mayer Maria , Ludewig Uwe
Published: March 2007

Ammonium transport across plant plasma membranes is facilitated by AMT/Rh-type ammonium transporters (AMTs), which also have homologs in most organisms. In the roots of the plant Arabidopsis (Arabidopsis thaliana), AMTs have been identified that function directly in the high-affinity NH4  + acquisition from soil. Here, we show that AtAMT1;2 has a distinct role, as it is located in the plasma membrane of the root endodermis. AtAMT1;2 functions as a comparatively low-affinity NH4  + transporter. Mutations at the highly conserved carboxyl terminus (C terminus) of AMTs, including one that mimics phosphorylation at a putative phosphorylation site, impair NH4  + transport activity. Coexpressing these mutants along with wild-type AtAMT1;2 substantially reduced the activity of the wild-type transporter. A molecular model of AtAMT1;2 provides a plausible explanation for the dominant inhibition, as the C terminus of one monomer directly contacts the neighboring subunit. It is suggested that part of the cytoplasmic C terminus of a single monomer can gate the AMT trimer. This regulatory mechanism for rapid and efficient inactivation of NH4  + transporters may apply to several AMT members to prevent excess influx of cytotoxic ammonium.
PIC1, an Ancient Permease in Arabidopsis Chloroplasts, Mediates Iron Transport
Authors: Duy Daniela , Wanner Gerhard , Meda Anderson R. , von Wirén Nicolaus , Soll Jürgen , Philippar Katrin
Published: March 2007

In chloroplasts, the transition metals iron and copper play an essential role in photosynthetic electron transport and act as cofactors for superoxide dismutases. Iron is essential for chlorophyll biosynthesis, and ferritin clusters in plastids store iron during germination, development, and iron stress. Thus, plastidic homeostasis of transition metals, in particular of iron, is crucial for chloroplast as well as plant development. However, very little is known about iron uptake by chloroplasts. Arabidopsis thaliana PERMEASE IN CHLOROPLASTS1 (PIC1), identified in a screen for metal transporters in plastids, contains four predicted α-helices, is targeted to the inner envelope, and displays homology with cyanobacterial permease-like proteins. Knockout mutants of PIC1 grew only heterotrophically and were characterized by a chlorotic and dwarfish phenotype reminiscent of iron-deficient plants. Ultrastructural analysis of plastids revealed severely impaired chloroplast development and a striking increase in ferritin clusters. Besides upregulation of ferritin, pic1 mutants showed differential regulation of genes and proteins related to iron stress or transport, photosynthesis, and Fe-S cluster biogenesis. Furthermore, PIC1 and its cyanobacterial homolog mediated iron accumulation in an iron uptake–defective yeast mutant. These observations suggest that PIC1 functions in iron transport across the inner envelope of chloroplasts and hence in cellular metal homeostasis.
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development
Authors: Lee Jungeun , He Kun , Stolc Viktor , Lee Horim , Figueroa Pablo , Gao Ying , Tongprasit Waraporn , Zhao Hongyu , Lee Ilha , Deng Xing Wang
Published: March 2007

The transcription factor LONG HYPOCOTYL5 (HY5) acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here, we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using a high-density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis thaliana genome, we mapped genome-wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed >3000 chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light-responsive genes and transcription factor genes. Our data thus support a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis.
Actively Growing Bacteria in the Inland Sea of Japan, Identified by Combined Bromodeoxyuridine Immunocapture and Denaturing Gradient Gel Electrophoresis
Authors: Hamasaki Koji , Taniguchi Akito , Tada Yuya , Long Richard A. , Azam Farooq
Published: March 2007

A fundamental question in microbial oceanography concerns the relationship between prokaryote diversity and biogeochemical function in an ecosystem context. We combined bromodeoxyuridine (BrdU) magnetic bead immunocapture and PCR-denaturing gradient gel electrophoresis (BUMP-DGGE) to examine phylotype-specific growth in natural marine assemblages. We also examined a broad range of marine bacterial isolates to determine their abilities to incorporate BrdU in order to test the validity of the method for application to diverse marine assemblages. We found that 27 of 29 isolates belonging to different taxa could incorporate BrdU. BUMP-DGGE analysis revealed phylogenetic affiliations of DNA-synthesizing, presumably actively growing bacteria across a eutrophic to mesotrophic transect in the Inland Sea of Japan. We found that the BrdU-incorporating (growing) communities were substantially different from the total communities. The majority (34/56) of phylotypes incorporated BrdU and were presumably growing, and these phylotypes comprised 10 alphaproteobacteria, 1 betaproteobacterium, 11 gammaproteobacteria, 11
Cytophaga-Flavobacterium-Bacteroides
group bacteria, and 1 unclassified bacterium. All BrdU-responsive alphaproteobacteria were members of the
Rhodobacterales
, suggesting that such bacteria were dominant in the growing alphaproteobacterial populations in our samples. The BrdU-responsive gammaproteobacteria belonged to the
Oceanospirillales
, the SAR86 cluster, the
Pseudomonadales
, the
Alteromonadales
, and the
Vibrionales
. Thus, contemporaneous cooccurrence of diverse actively growing bacterial taxa was a consistent pattern in our biogeochemically varied study area.
Refined Medium for Direct Isolation of
Vibrio vulnificus
from Oyster Tissue and Seawater
Authors: Warner Elizabeth , Oliver James D.
Published: March 2007

We have developed a new medium for the direct isolation of
Vibrio vulnificus
from water and oyster samples. The medium was shown in laboratory and field studies to be highly selective without providing preferential isolation of either
V. vulnificus
genotype.
First Evidence of Division and Accumulation of Viable but Nonculturable
Pseudomonas fluorescens
Cells on Surfaces Subjected to Conditions Encountered at Meat Processing Premises
Authors: Peneau Sophie , Chassaing Danielle , Carpentier Brigitte
Published: March 2007

Cleaning and disinfection of open surfaces in food industry premises leave some microorganisms behind; these microorganisms build up a resident flora on the surfaces. Our goal was to explore the phenomena involved in the establishment of this biofilm. Ceramic coupons were contaminated, once only, with
Pseudomonas fluorescens
suspended in meat exudate incubated at 10°C. The mean adhering population after 1 day was 10
2
CFU·cm
−2
and 10
3
total cells·cm
−2
, i.e., the total number of cells stained by DAPI (4′,6′-diamidino-2-phenylindole). The coupons were subjected daily to a cleaning product, a disinfectant, and a further soiling with exudate. The result was a striking difference between the numbers of CFU, which reached 10
4
CFU·cm
−2
, and the numbers of total cells, which reached 2 × 10
6
cells·cm
−2
in 10 days. By using hypotheses all leading to an overestimation of the number of dead cells, we showed that the quantity of nonculturable cells (DAPI-positive cells minus CFU) observed cannot be accounted for as an accumulation of dead cells. Some nonculturable cells are therefore dividing on the surface, although cell division is unable to continue to the stage of macrocolony formation on agar. The same phenomenon was observed when only a chlorinated alkaline product was used and the number of cells capable of reducing 5-cyano-2,3-ditolyl tetrazolium chloride was close to the number of total cells, confirming that most nonculturable cells are viable but nonculturable. Furthermore, the daily shock applied to the cells does not prompt them to enter a new lag phase. Since a single application of microorganisms is sufficient to produce this accumulation of cells, it appears that the phenomenon is inevitable on open surfaces in food industry premises.
Diversity and Metabolism of Marine Bacteria Cultivated on Dissolved DNA
Authors: Lennon Jay T.
Published: March 2007

Dissolved DNA (dDNA) is a potentially important source of energy and nutrients in aquatic ecosystems. However, little is known about the identity, metabolism, and interactions of the microorganisms capable of consuming dDNA. Bacteria from Eel Pond (Woods Hole, MA) were cultivated on low-molecular-weight (LMW) or high-molecular-weight (HMW) dDNA, which served as the primary source of carbon, nitrogen, and phosphorus. Cloning and sequencing of 16S rRNA genes revealed that distinct bacterial assemblages with comparable levels of taxon richness developed on LMW and HMW dDNA. Since the LMW and HMW dDNA used in this study were stoichiometrically identical, the results confirm that the size alone of dissolved organic matter can influence bacterial community composition. Variation in the growth and metabolism of isolates provided insight into mechanisms that may have generated differences in bacterial community composition. For example, bacteria from LMW dDNA enrichments generally grew better on LMW dDNA than on HMW dDNA. In contrast, bacteria isolated from HMW dDNA enrichments were more effective at degrading HMW dDNA than bacteria isolated from LMW dDNA enrichments. Thus, marine bacteria may experience a trade-off between their ability to compete for LMW dDNA and their ability to access HMW dDNA via extracellular nuclease production. Together, the results of this study suggest that dDNA turnover in marine ecosystems may involve a succession of microbial assemblages with specialized ecological strategies.
Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Newly Isolated Carbazole-Degrading
Sphingomonas
sp. Strain
Authors: Gai Zhonghui , Yu Bo , Li Li , Wang Ying , Ma Cuiqing , Feng Jinhui , Deng Zixin , Xu Ping
Published: March 2007

A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated
Sphingomonas
sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways.
Sphingomonas
sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.
Transcriptional Response ofSaccharomyces cerevisiaeto Different Nitrogen Concentrations during Alcoholic Fermentation
Authors: Mendes-Ferreira A. , del Olmo M. , García-Martínez J. , Jiménez-Martí E. , Mendes-Faia A. , Pérez-Ortín J. E. , Leão C.
Published: March 2007

Gene expression profiles of a wine strain ofSaccharomyces cerevisiaePYCC4072 were monitored during alcoholic fermentations with three different nitrogen supplies: (i) control fermentation (with enough nitrogen to complete sugar fermentation), (ii) nitrogen-limiting fermentation, and (iii) the addition of nitrogen to the nitrogen-limiting fermentation (refed fermentation). Approximately 70% of the yeast transcriptome was altered in at least one of the fermentation stages studied, revealing the continuous adjustment of yeast cells to stressful conditions. Nitrogen concentration had a decisive effect on gene expression during fermentation. The largest changes in transcription profiles were observed when the early time points of the N-limiting and control fermentations were compared. Despite the high levels of glucose present in the media, the early responses of yeast cells to low nitrogen were characterized by the induction of genes involved in oxidative glucose metabolism, including a significant number of mitochondrial associated genes resembling the yeast cell response to glucose starvation. As the N-limiting fermentation progressed, a general downregulation of genes associated with catabolism was observed. Surprisingly, genes encoding ribosomal proteins and involved in ribosome biogenesis showed a slight increase during N starvation; besides, genes that comprise theRiBiregulon behaved distinctively under the different experimental conditions. Here, for the first time, the global response of nitrogen-depleted cells to nitrogen addition under enological conditions is described. An important gene expression reprogramming occurred after nitrogen addition; this reprogramming affected genes involved in glycolysis, thiamine metabolism, and energy pathways, which enabled the yeast strain to overcome the previous nitrogen starvation stress and restart alcoholic fermentation.
Cloning, Characterization, and Molecular Application of a Beta-Agarase Gene fromVibriosp. Strain V134
Authors: Zhang Wei-wei , Sun Li
Published: March 2007

V134, a marine isolate of theVibriogenus, was found to produce a new beta-agarase of the GH16 family. The relevant agarase geneagaVwas cloned from V134 and conditionally expressed inEscherichia coli. Enzyme activity analysis revealed that the optimum temperature and pH for the purified recombinant agarase were around 40°C and 7.0. AgaV was demonstrated to be useful in two aspects: first, as an agarolytic enzyme, the purified recombinant AgaV could be employed in the recovery of DNA from agarose gels; second, as a secretion protein, AgaV was explored at the genetic level and used as a reporter in the construction of a secretion signal trap which proved to be a simple and efficient molecular tool for the selection of genes encoding secretion proteins from both gram-positive and gram-negative bacteria.
Antisense RNA Modulation of Alkyl Hydroperoxide Reductase Levels in
Helicobacter pylori
Correlates with Organic Peroxide Toxicity but Not Infectivity
Authors: Croxen Matthew A. , Ernst Peter B. , Hoffman Paul S.
Published: March 2007

Much of the gene content of the human gastric pathogen
Helicobacter pylori
(∼1.7-Mb genome) is considered essential. This view is based on the completeness of metabolic pathways, infrequency of nutritional auxotrophies, and paucity of pathway redundancies typically found in bacteria with larger genomes. Thus, genetic analysis of gene function is often hampered by lethality. In the absence of controllable promoters, often used to titrate gene function, we investigated the feasibility of an antisense RNA interference strategy. To test the antisense approach, we targeted alkyl hydroperoxide reductase (AhpC), one of the most abundant proteins expressed by
H. pylori
and one whose function is essential for both in vitro growth and gastric colonization. Here, we show that antisense
ahpC
(as-
ahpC
) RNA expression from shuttle vector pDH37::as-
ahpC
achieved an ∼72% knockdown of AhpC protein levels, which correlated with increased susceptibilities to hydrogen peroxide, cumene, and
tert
-butyl hydroperoxides but not with growth efficiency. Compensatory increases in catalase levels were not observed in the knockdowns. Expression of single-copy antisense constructs (expressed under the urease promoter and containing an fd phage terminator) from the
rdxA
locus of mouse-colonizing strain X47 achieved a 32% knockdown of AhpC protein levels (relative to wild-type X47 levels), which correlated with increased susceptibility to organic peroxides but not with mouse colonization efficiency. Our studies indicate that high levels of AhpC are not required for in vitro growth or for primary gastric colonization. Perhaps AhpC, like catalase, assumes a greater role in combating exogenous peroxides arising from lifelong chronic inflammation. These studies also demonstrate the utility of antisense RNA interference in the evaluation of gene function in
H. pylori
.