bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleolar size in choroidal and ciliary body melanomas and corresponding hepatic metastases
Authors: Al‐Jamal Rana’a T. , Toivonen Päivi , Kivelä Tero 
Published: June 2009

Abstract.Purpose:  This study aimed to investigate the relationship between hepatic metastasis and the mean diameter of the 10 largest nucleoli (MLN) in uveal melanoma.Methods:  A cross‐sectional histopathological analysis of 37 metastases (13 surgical or needle biopsies, 24 autopsies) and corresponding primary choroidal and ciliary body melanomas was conducted, using statistical tests appropriate for paired data. The largest nucleoli were measured from digital photographs of silver‐stained sections along a 5‐mm‐wide linear field. Confounders considered were presence of epithelioid cells and microvascular density (MVD), counted as the number of discrete elements labelled by monoclonal antibody QBEND/10 to the CD34 epitope.Results:  Hepatic metastases had more frequent epithelioid cells (p = 0.0047) and a higher MVD (median difference, 7.5 counts/0.313 mm2 more; p = 0.044) than their corresponding primary tumours. Hepatic metastases, especially in autopsy specimens rather than surgical biopsies, tended to have a smaller MLN (median 3.6 μm) than the corresponding primary tumour (median difference, 0.55 μm; p = 0.066). The MLN in hepatic metastases was not associated with presence of epithelioid cells and MVD. Overall survival after diagnosis of metastasis was comparable whether hepatic metastases had a large or small MLN (p = 0.95), whereas a high MVD tended to be associated with shorter survival (p = 0.096) among the 13 patients with known survival.Conclusions:  The results suggest that MLN is not a useful marker for assessing prognosis after diagnosis of hepatic metastasis from uveal melanoma.
The inhibitory effect of different concentrations of topical bevacizumab on corneal neovascularization
Authors: Habot‐Wilner Zohar , Barequet Irina S. , Ivanir Yair , Moisseiev Joseph , Rosner Mordechai 
Published: June 2009

Acta Ophthalmol. 2010: 88: 862–867Abstract.Purpose:  This study aimed to evaluate the effects of different concentrations of topically administered bevacizumab (Avastin) on experimental corneal neovascularization (NV) in rats.Methods:  Corneal NV was induced by chemical cauterization with silver nitrate sticks applied to the centre of the corneas of 37 Wistar rats. The rats were then randomized to four topical treatment groups: group 1 (n = 10) received 4 mg/ml bevacizumab; group 2 (n = 9) received 2 mg/ml bevacizumab; group 3 (n = 10) received 1 mg/ml bevacizumab, and group 4 (n = 8) represented a control group and received saline. All drops were initiated immediately after cauterization and applied twice per day for 7 days. Corneal NV was assessed 8 days after cauterization in a masked fashion, both qualitatively by clinical evaluation and quantitatively by blood vessel count in photographs of histological sections.Results:  On clinical evaluation, groups 1 and 2 showed significantly less NV compared with the saline‐treated control group (p = 0.006 and p = 0.024, respectively). Histopathological evaluation showed that only group 1 differed significantly from controls (5% significance level) and normal corneal epithelium was seen in all groups.Conclusions:  Topically administered bevacizumab at a concentration of 4 mg/ml significantly reduces corneal NV according to both clinical and histopathological evaluations; lower concentrations were less effective on both parameters. No corneal epitheliopathy was found using these concentrations.
Escherichia coli
O157:H7 Strain Origin, Lineage, and Shiga Toxin 2 Expression Affect Colonization of Cattle
Authors: Lowe Ross M. S. , Baines Danica , Selinger L. Brent , Thomas James E. , McAllister Tim A. , Sharma Ranjana 
Published: June 2009

ABSTRACT

Enterohemorrhagic
Escherichia coli
O157:H7 has evolved into an important human pathogen with cattle as the main reservoir. The recent discovery of
E. coli
O157:H7-induced pathologies in challenged cattle has suggested that previously discounted bacterial virulence factors may contribute to the colonization of cattle. The objective of the present study was to examine the impact of lineage type, cytotoxin activity, and cytotoxin expression on the amount of
E. coli
O157:H7 colonization of cattle tissue and cells in vitro. Using selected bovine- and human-origin strains, we determined that lineage type predicted the amount of
E. coli
O157:H7 strain colonization: lineage I > intermediate lineages > lineage II. All
E. coli
O157:H7 strain colonization was dose dependent, with threshold colonization at 10
3
to 10
5
CFU and maximum colonization at 10
7
CFU. We also determined that an as-yet-unknown factor of strain origin was the most dominant predictor of the amount of strain colonization in vitro. The amount of
E. coli
O157:H7 colonization was also influenced by strain cytotoxin activity and the inclusion of cytotoxins from lineage I or intermediate lineage strains increased colonization of a lineage II strain. There was a higher level of expression of the Shiga toxin 1 gene (
stx
1
) in human-origin strains than in bovine-origin strains. In addition, lineage I strains expressed higher levels of the Shiga toxin 2 gene (
stx
2
). The present study supports a role for strain origin, lineage type, cytotoxin activity, and
stx
2
expression in modulating the amount of
E. coli
O157:H7 colonization of cattle.
Detection and Enumeration ofClostridium difficileSpores in Retail Beef and Pork
Authors: Weese J. Scott , Avery Brent P. , Rousseau J. , Reid-Smith Richard J. 
Published: June 2009

ABSTRACTRecent studies have identifiedClostridium difficilein food animals and retail meat, and concern has been raised about the potential for food to act as a source ofC. difficileinfection in humans. Previous studies of retail meat have relied on enrichment culture alone, thereby preventing any assessment of the level of contamination in meat. This study evaluated the prevalence ofC. difficilecontamination of retail ground beef and ground pork in Canada. Ground beef and ground pork were purchased from retail outlets in four Canadian provinces. Quantitative and enrichment culture was performed.Clostridium difficilewas isolated from 28/230 (12%) samples overall: 14/115 (12%) ground beef samples and 14/115 (12%) ground pork samples (P= 1.0). For ground beef, 10/14 samples (71%) were positive by enrichment culture only. Of the 4 ground beef samples that were positive by direct culture, 20 spores/g were present in 2 while 120 and 240 spores/g were present in 1 each. For ground pork, 10/14 (71%) samples were positive by enrichment culture only. Of the 4 ground pork samples that were positive by direct culture, 20 spores/g were present in 3 while 60 spores/g were present in 1. Ribotype 078 predominated, consistent with some previous studies ofC. difficilein food animals. Ribotype 027/North American pulsotype 1 was also identified in both retail beef and pork. This study has identified relatively common contamination of retail ground beef and pork withC. difficilespores; however, the levels of contamination were very low.
Prevalence and Genotypes of Human Noroviruses in Tropical Urban Surface Waters and Clinical Samples in Singapore
Authors: Aw Tiong Gim , Gin Karina Yew-Hoong , Ean Oon Lynette Lin , Chen Eileen Xueqin , Woo Chee Hoe 
Published: June 2009

ABSTRACT
The prevalence and genotypes of norovirus genogroup I (GI) and GII in tropical urban catchment waters and an estuarine bay were studied. A comparative analysis was performed with environmental isolates of noroviruses and concurrently identified clinical isolates in Singapore during gastroenteritis outbreaks between August 2006 to January 2007. Noroviruses in environmental water samples were concentrated by using ultrafiltration techniques and then analyzed by reverse transcription-seminested PCR assay targeting the partial capsid region of noroviruses and DNA sequencing. Among the 60 water samples collected, noroviruses were detected in 43 (71.7%) of these samples. Of these 43 norovirus-positive samples, the coexistence of both GI and GII strains was identified in 23 (53.5%) water samples. The phylogenetic analysis revealed multiple genotypes of noroviruses GI and GII in environmental water samples. GI and GII strains were clustered into seven and nine (including two unclassified) genotypes, respectively. The major norovirus genotypes in environmental water samples were GI/2 and GI/4 and GII/4. Genotyping of the 21 norovirus-positive clinical samples showed that all of the strains belonged to the GII/4 cluster. The environmental and clinical norovirus GII/4 isolates showed high levels of nucleotide sequence identity to each other and to the novel GII/4 variant associated with global epidemics of gastroenteritis during 2006. This study suggests the emergence and circulation of multiple novel norovirus GI and GII genotypes in water environments. Further comprehensive surveillance of water environments for noroviruses and routine clinical reporting is warranted.
Characterization of the Central Metabolic Pathways in
Thermoanaerobacter
sp. Strain X514 via Isotopomer-Assisted Metabolite Analysis
Authors: Feng Xueyang , Mouttaki Housna , Lin Lu , Huang Rick , Wu Bing , Hemme Christopher L. , He Zhili , Zhang Baichen , Hicks Leslie M. , Xu Jian , Zhou Jizhong , Tang Yinjie J. 
Published: June 2009

ABSTRACT

Thermoanaerobacter
sp. strain X514 has great potential in biotechnology due to its capacity to ferment a range of C
5
and C
6
sugars to ethanol and other metabolites under thermophilic conditions. This study investigated the central metabolism of strain X514 via
13
C-labeled tracer experiments using either glucose or pyruvate as both carbon and energy sources. X514 grew on minimal medium and thus contains complete biosynthesis pathways for all macromolecule building blocks. Based on genome annotation and isotopic analysis of amino acids, three observations can be obtained about the central metabolic pathways in X514. First, the oxidative pentose phosphate pathway in X514 is not functional, and the tricarboxylic acid cycle is incomplete under fermentative growth conditions. Second, X514 contains (
Re
)-type citrate synthase activity, although no gene homologous to the recently characterized (
Re
)-type citrate synthase of
Clostridium kluyveri
was found. Third, the isoleucine in X514 is derived from acetyl coenzyme A and pyruvate via the citramalate pathway rather than being synthesized from threonine via threonine ammonia-lyase. The functionality of the citramalate synthase gene (
cimA
[Teth514_1204]) has been confirmed by enzymatic activity assays, while the presence of intracellular citramalate has been detected by mass spectrometry. This study demonstrates the merits of combining
13
C-assisted metabolite analysis, enzyme assays, and metabolite detection not only to examine genome sequence annotations but also to discover novel enzyme activities.
Effect of Nitrate and Acetylene on
nirS
,
cnorB
, and
nosZ
Expression and Denitrification Activity in
Pseudomonas mandelii
Authors: Saleh-Lakha Saleema , Shannon Kelly E. , Henderson Sherri L. , Zebarth Bernie J. , Burton David L. , Goyer Claudia , Trevors Jack T. 
Published: June 2009

ABSTRACT

Nitrate acts as an electron acceptor in the denitrification process. The effect of nitrate in the range of 0 to 1,000 mg/liter on
Pseudomonas mandelii nirS
,
cnorB
, and
nosZ
gene expression was studied, using quantitative reverse transcription-quantitative PCR. Denitrification activity was measured by using the acetylene blockage method and gas chromatography. The effect of acetylene on gene expression was assessed by comparing denitrification gene expression in
P. mandelii
culture grown in the presence or absence of acetylene. The higher the amount of NO
3
−
present, the greater the induction and the longer the denitrification genes remained expressed.
nirS
gene expression reached a maximum at 2, 4, 4, and 6 h in cultures grown in the presence of 0, 10, 100, and 1,000 mg of KNO
3
/liter, respectively, while induction of
nirS
gene ranged from 12- to 225-fold compared to time zero.
cnorB
gene expression also followed a similar trend.
nosZ
gene expression did not respond to NO
3
−
treatment under the conditions tested. Acetylene decreased
nosZ
gene expression but did not affect
nirS
or
cnorB
gene expression. These results showed that
nirS
and
cnorB
responded to nitrate concentrations; however, significant denitrification activity was only observed in culture with 1,000 mg of KNO
3
/liter, indicating that there was no relationship between gene expression and denitrification activity under the conditions tested.
Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups
Authors: Marti Romain , Dabert Patrick , Pourcher Anne-Marie 
Published: June 2009

ABSTRACT

The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of
Bacteroides
-
Prevotella
,
Eubacterium
-
Clostridiaceae
,
Bacillus
-
Streptococcus
-
Lactobacillus
(BSL), and
Bifidobacterium
group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that
Bifidobacterium
spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either
Eubacterium
-
Clostridiaceae
or
Bacteroides
-
Prevotella
. Two
Bifidobacterium
species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species,
Bifidobacterium thermacidophilum
subsp.
porcinum
, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination.
Identification of anaoxSystem That Requires Cytochromecin the Highly Arsenic-Resistant BacteriumOchrobactrum triticiSCII24
Authors: Branco Rita , Francisco Romeu , Chung Ana Paula , Morais Paula Vasconcelos 
Published: June 2009

ABSTRACTMicrobial biotransformations have a major impact on environments contaminated with toxic elements, including arsenic, resulting in an increasing interest in strategies responsible for how bacteria cope with arsenic. In the present work, we investigated the metabolism of this metalloid in the bacteriumOchrobactrum triticiSCII24. This heterotrophic organism contains two differentarsoperons and is able to oxidize arsenite to arsenate. The presence of arsenite oxidase genes in this organism was evaluated, and sequence analysis revealed structural genes for an As(III) oxidase (aoxAB), ac-type cytochrome (cytC), and molybdopterin biosynthesis (moeA). Two other genes coding for a two-component signal transduction pair (aoxRS) were also identified upstream from the previous gene cluster. The involvement ofaoxgenes in As(III) oxidation was confirmed by functionally expressing them intoO. tritici5bvl1, a non-As(III) oxidizer. Experiments showed that the As(III) oxidation process inO. triticirequires not only the enzyme arsenite oxidase but also the cytochromecencoded in the operon. The fundamental role of this cytochromec, reduced in the presence of arsenite in strain SCII24 but not in anO. triticiΔaoxBmutant, is surprising, since to date this feature has not been found in other organisms. In this strain the presence of anaoxsystem does not seem to confer an additional arsenite resistance capability; however, it might act as part of an As(III)-detoxifying strategy. Such mechanisms may have played a crucial role in the development of early stages of life on Earth and may one day be exploited as part of a potential bioremediation strategy in toxic environments.
Glycerol-3-Phosphate Acyltransferases Gat1p and Gat2p Are Microsomal Phosphoproteins with Differential Contributions to Polarized Cell Growth
Authors: Bratschi Martin W. , Burrowes David P. , Kulaga Adam , Cheung Jing F. , Alvarez Ana L. , Kearley Jennifer , Zaremberg Vanina 
Published: June 2009

ABSTRACT

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the initial step in the synthesis of all glycerolipids. It is the committed and rate-limiting step and is redundant in
Saccharomyces cerevisiae
, mammals, and plants. GPAT controls the formation of lipid intermediates that serve not only as precursors of more-complex lipids but also as intracellular signaling molecules.
Saccharomyces cerevisiae
possesses two GPATs, encoded by the
GAT1
and
GAT2
genes. Metabolic analysis of yeast lacking either
GAT1
or
GAT2
indicated partitioning of the two main branches of phospholipid synthesis at the initial and rate-limiting GPAT step. We are particularly interested in identifying molecular determinants mediating lipid metabolic pathway partitioning; therefore, as a starting point, we have performed a detailed study of Gat1p and Gat2p cellular localization. We have compared Gat1p and Gat2p localization by fluorescence microscopy and subcellular fractionation using equilibrium density gradients. Our results indicate Gat1p and Gat2p overlap mostly in their localization and are in fact microsomal GPATs, localized to both perinuclear and cortical endoplasmic reticula in actively proliferating cells. A more detailed analysis suggests a differential enrichment of Gat1p and Gat2p in distinct ER fractions. Furthermore, overexpression of these enzymes in the absence of endogenous GPATs induces proliferation of distinct ER arrays, differentially affecting cortical ER morphology and polarized cell growth. In addition, our studies also uncovered a dynamic posttranslational regulation of Gat1p and Gat2p and a compensation mechanism through phosphorylation that responds to a cellular GPAT imbalance.
Cooperative Regulation of
ADE3
Transcription by Gcn4p and Bas1p in
Saccharomyces cerevisiae
Authors: Joo Yoo Jin , Kim Jung-Ae , Baek Joung Hee , Seong Ki Moon , Han Kyung-Duk , Song Jae Mahn , Choi Jin Young , Kim Joon 
Published: June 2009

ABSTRACT

The one-carbon response regulon is essential for the biosynthesis of nucleic acids as well as several amino acids. The
ADE3
gene is known to encode a crucial one-carbon regulon enzyme, tetrahydrofolate synthase, which is involved in the biosynthesis of purine and the amino acids methionine and glycine. Therefore, the mechanism through which
ADE3
transcription is regulated appears to be critical for the cross-talk among these metabolic pathways. Even so, the direct involvement of
ADE3
transcription through gene-specific transcription factors has not been shown clearly. In this study, the promoter structure of the
ADE3
gene was investigated in detail, and a genuine Gcn4p responsive element (GCRE) was confirmed among three putative GCRE elements in vivo and in vitro. Through gene deletion studies of Gcn4p and Bas1p, it was established that both factors are involved in the transcriptional regulation of the
ADE3
gene. Direct binding to this GCRE and the occupancy of the
ADE3
promoter by these factors were also confirmed. Taking these results together, we concluded that Gcn4p is responsible for the basal and inducible expression of the
ADE3
gene, while Bas1p is required for its basal expression.
Roles of the Glyoxylate and Methylcitrate Cycles in Sexual Development and Virulence in the Cereal PathogenGibberella zeae
Authors: Lee Seung-Ho , Han You-Kyoung , Yun Sung-Hwan , Lee Yin-Won 
Published: June 2009

ABSTRACTThe glyoxylate and methylcitrate cycles are involved in the metabolism of two- or three-carbon compounds in fungi. To elucidate the role(s) of these pathways inGibberella zeae, which causes head blight in cereal crops, we focused on the functions ofG. zeaeorthologs (GzICL1and GzMCL1) of the genes that encode isocitrate lyase (ICL) and methylisocitrate lyase (MCL), respectively, key enzymes in each cycle. The deletion of GzICL1(ΔGzICL1) caused defects in growth on acetate and in perithecium (sexual fruiting body) formation but not in virulence on barley and wheat, indicating that GzICL1 acts as the ICL of the glyoxylate cycle and is essential for self-fertility inG. zeae. In contrast, the ΔGzMCL1strains failed to grow on propionate but exhibited no major changes in other traits, suggesting that GzMCL1 is required for the methylcitrate cycle inG. zeae. Interestingly, double deletion of both GzICL1and GzMCL1caused significantly reduced virulence on host plants, indicating that both GzICL1and GzMCL1have redundant functions for plant infection inG. zeae. Thus, both GzICL1and GzMCL1may play important roles in determining major mycological and pathological traits ofG. zeaeby participating in different metabolic pathways for the use of fatty acids.
Investigation of Carbon Metabolism in “
Dehalococcoides ethenogenes
” Strain 195 by Use of Isotopomer and Transcriptomic Analyses
Authors: Tang Yinjie J. , Yi Shan , Zhuang Wei-Qin , Zinder Stephen H. , Keasling Jay D. , Alvarez-Cohen Lisa 
Published: June 2009

ABSTRACT

Members of the genus “
Dehalococcoides
” are the only known microorganisms that can completely dechlorinate tetrachloroethene and trichloroethene to the innocuous end product, ethene. This study examines the central metabolism in “
Dehalococcoides ethenogenes
” strain 195 via
13
C-labeled tracer experiments. Supported by the genome annotation and the transcript profile, isotopomer analysis of key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic pathway in strain 195. First, the
13
C-labeling studies revealed that strain 195 contains complete amino acid biosynthesis pathways, even though current genome annotation suggests that several of these pathways are incomplete. Second, the tricarboxylic acid cycle of strain 195 is confirmed to be branched, and the Wood-Ljungdahl carbon fixation pathway is shown to not be functionally active under our experimental conditions; rather, CO
2
is assimilated via two reactions, conversion of acetyl-coenzyme A (acetyl coenzyme A [acetyl-CoA]) to pyruvate catalyzed by pyruvate synthase (DET0724-0727) and pyruvate conversion to oxaloacetate via pyruvate carboxylase (DET0119-0120). Third, the
13
C-labeling studies also suggested that isoleucine is synthesized from acetyl-CoA and pyruvate via citramalate synthase (CimA, EC 2.3.1.182), rather than from the common pathway via threonine ammonia-lyase (EC 4.3.1.19). Finally, evidence is presented that strain 195 may contain an undocumented citrate synthase (>95%
Re
-type stereospecific), i.e., a novel
Re
-citrate synthase that is apparently different from the one recently reported in
Clostridium kluyveri
.
Identification and Characterization ofgshA, a Gene Encoding the Glutamate-Cysteine Ligase in the Halophilic ArchaeonHaloferax volcanii
Authors: Malki Liron , Yanku Michaela , Borovok Ilya , Cohen Gerald , Mevarech Moshe , Aharonowitz Yair 
Published: June 2009

ABSTRACTHalophilic archaea were found to contain in their cytoplasm millimolar concentrations of γ-glutamylcysteine (γGC) instead of glutathione. Previous analysis of the genome sequence of the archaeonHalobacteriumsp. strain NRC-1 has indicated the presence of a sequence homologous to sequences known to encode the glutamate-cysteine ligase GshA. We report here the identification of thegshAgene in the extremely halophilic archaeonHaloferax volcaniiand show thatH. volcanii gshAdirects in vivo the synthesis and accumulation of γGC. We also show that theH. volcaniigene when expressed in anEscherichia colistrain lacking functional GshA is able to restore synthesis of glutathione.