bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trisomy 12 mosaicism detected by mid–trimester amniocentesis
Authors: Petrella Rena , Hirschhorn Kurt 
Published: March 2007

AbstractTrisomy 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

AbstractFirst‐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

AbstractIn 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

AbstractA 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

AbstractA 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.
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

AbstractA 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

Abstract
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

Abstract
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

AbstractThe 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 &gt;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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACTGene 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

ABSTRACTV134, 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

ABSTRACT

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
.