bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of DNA Content Parameters in Paired, Fresh Tissue Pretreatment Biopsies and Surgical Resections from Squamous Cell Carcinoma of the Head and Neck
Authors: Rayes B. F. EL , Maciorowski Z. , Pietraszkiewicz H. , Ensley J. F. 
Published: March 2003

OBJECTIVECellular DNA characteristics derived from pretreatment biopsy (PTB) may become important for predicting treatment outcomes in patients with head and neck squamous cell cancer (HNSCC). Whether the PTB adequately represents the whole specimen is of critical importance.STUDY DESIGNIn a series of >700 HNSCCs, we identified 59 cases in which the PTB and the surgical resection (SR) met the following criteria: PTB and SR were from the same site, and SR was obtained within 5 weeks of PTB with no intervening treatments.RESULTSTwenty‐nine percent of the PTB specimens were DNA diploid. Only 1 of the 11 subsequent DNA diploid SR was associated with a DNA aneuploid PTB (91% concordance). Of the 48 DNA aneuploid tumors, 3 were associated with DNA diploid PTB (94% concordance). Three other DNA aneuploid SRs were associated with PTB of poor quality.CONCLUSIONWith respect to DNA ploidy, PTB are representative of SR specimens.
Pain Intensity after Laseruvulopalatoplasty and Tonsillectomy
Authors: Kokki Hannu , Nikanne Elina , Aho Mikko , Virtaniemi Jukka 
Published: March 2003

OBJECTIVEThe first objective of this study was to evaluate pain intensity and opioid consumption during the first 24 hours after uvulopalatoplasty and tonsillectomy in the hospital, and the second was to evaluate pain intensity and its progression during the first 2 weeks after surgery at home.STUDY DESIGN AND SETTINGSIn a prospective parallel group study, 51 patients with uvulopalatoplasty or tonsillectomy were studied. Ketoprofen, a nonsteroidal antiinflammatory drug, and fentanyl citrate, an opioid, were used as analgesics.RESULTSDespite ketoprofen infusion and free access to a patient‐controlled pump with fentanyl citrate for rescue analgesia, inadequate pain relief was common both after uvulopalatoplasty (35%) and after tonsillectomy (28%) during the first 24 hours after surgery. The consumption of fentanyl citrate was similar after both operations. At home, pain intensity was highest in the mornings during the first 5 days, and 10 patients had some pain still after 2 weeks. Also at home, high pain scores were reported commonly in both groups.CONCLUSIONSgnificant pain after uvulopalatoplasty and tonsillectomy lasted for several days. Ketoprofen in the commercial capsule form proved to be too short acting for overnight pain relief.SIGNIFICANCEPain treatment in patients with uvulopalatoplasty and tonsillectomy should be improved to allow patients a peaceful recovery after surgery.
Anatomic Variations of the Arteries of the Nasal Fossa
Authors: Babin Emmanuel , Moreau Sylvain , de Rugy Marc Goullet , Delmas Pierre , Valdazo André , Bequignon Arnaud 
Published: March 2003

OBJECTIVEThis study was performed for knowledge about the vascular supply of the nasal fossa and a description of the site of division and number of branches of the sphenopalatine artery.STUDY DESIGNThis study was performed on 10 fresh nonembalmed cadavers. Anatomic variations of nasal fossa arteries were studied.METHODSFirst, 10 cephalic anatomic preparations were injected with red color latex into the right and left carotid arteries. Then, these specimens were sagittally cut to dissect the sphenopalatine artery. Twenty vascularization cases were studied for the external branch of the sphenopalatine artery, and 10 cases were studied for the internal branch.RESULTSThe principal observations were: 1, the sphenopalatine artery division is 18 times in the infratemporal fossa and twice in the nasal fossa; 2, the nasopalatine artery supplies blood to the lower part of the septum and its anterosuperior area; and 3, the vascularization of the external wall is via the sphenopalatine artery through the arteries of the meatus and conchae.CONCLUSIONThis study defines the vascular territories of the nasal fossa arteries and includes photographs of dissections.
Composite Chondroperichondrial Clip Tympanoplasty: The Triple “C” Technique
Authors: Sylvester Valentine Fernandes 
Published: March 2003

OBJECTIVESThe study goal was to assess the success rate and efficacy of a myringoplasty (tympanoplasty type I) technique using a composite chondroperichondrial graft in a combined overlayunderlay fashion.STUDY DESIGNA retrospective analysis of patients subjected to the technique was conducted.METHODSA sample of 15 patients who met the inclusion criteria were reviewed for surgical results. All patients were treated by a single surgeon.RESULTSThis transcanal technique provides minimal morbidity and excellent results in selected patients.CONCLUSIONSThe described technique provides an effective method of closing nonmarginal perforations of the tympanic membrane.
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Authors: Kim Heenam , Snesrud Erik C. , Haas Brian , Cheung Foo , Town Christopher D. , Quackenbush John 
Published: March 2003

The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plantArabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3′ ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.[The sequence data from this study have been submitted to ArrayExpress under accession nos.: For the Array Design, A-TIGR-2. For the three subgroups of experiments: AbioticStress, E-TIGR-2; BioticStress, E-TIGR-3; Tissues, E-TIGR-4.]
Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates
Authors: Frazer Kelly A. , Chen Xiyin , Hinds David A. , Pant P.V. Krishna , Patil Nila , Cox David R. 
Published: March 2003

Comparative DNA sequence studies between humans and nonhuman primates will be important for understanding the genetic basis of the phenotypic differences between these species. Here we compare ∼27 Mb of human chromosome 21 with chimpanzee DNA sequences identifying 57 genomic rearrangements (deletions and insertions ranging in size from 0.2 to 8.0 kb) between the two species. These rearrangements are distributed along the entire length of chromosome 21, with ∼35% found in genomic intervals encoding genes (genic intervals), and have occurred in the genomes of both humans and chimpanzees. Comparison of ∼9 Mb of human chromosome 21 with orangutan, rhesus macaque, and woolly monkey DNA sequences identified a combined total of 114 genomic rearrangements between humans and nonhuman primates. Analysis of these rearrangements revealed that they are randomly distributed with respect to genic and nongenic intervals and identified one deletion that has likely resulted in the inactivation of a gene (β1,3-galactosyltransferase) in the woolly monkey. Our data show that genomic rearrangements have occurred frequently during primate genome evolution and significantly contribute to the DNA differences between these species. These DNA rearrangements are commonly found in genic intervals, and thus provide natural starting points for focused investigations of qualitative and quantitative gene expression differences between humans and other primates.[Supplemental material is available online atwww.genome.org.]
Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae
Authors: Rowe-Magnus Dean A. , Guerout Anne-Marie , Biskri Latefa , Bouige Philippe , Mazel Didier 
Published: March 2003

Integrons are natural tools for bacterial evolution and innovation. Their involvement in the capture and dissemination of antibiotic-resistance genes among Gram-negative bacteria is well documented. Recently, massive ancestral versions, the superintegrons (SIs), were discovered in the genomes of diverse proteobacterial species. SI gene cassettes with an identifiable activity encode proteins related to simple adaptive functions, including resistance, virulence, and metabolic activities, and their recruitment was interpreted as providing the host with an adaptive advantage. Here, we present extensive comparative analysis of SIs identified among the Vibrionaceae. Each was at least 100 kb in size, reaffirming the participation of SIs in the genome plasticity and heterogeneity of these species. Phylogenetic and localization data supported the sedentary nature of the functional integron platform and its coevolution with the host genome. Conversely, comparative analysis of the SI cassettes was indicative of both a wide range of origin for the entrapped genes and of an active cassette assembly process in these bacterial species. The signature attC sites of each species displayed conserved structural characteristics indicating that symmetry rather than sequence was important in the recognition of such a varied collection of target recombination sequences by a single site-specific recombinase. Our discovery of various addiction module cassettes within each of the different SIs indicates a possible role for them in the overall stability of large integron cassette arrays.[Supplemental material is available online atwww.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. listed in Table 1.]
Genome Duplication, a Trait Shared by 22,000 Species of Ray-Finned Fish
Authors: Taylor John S. , Braasch Ingo , Frickey Tancred , Meyer Axel , Van de Peer Yves 
Published: March 2003

Through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies in the tetraploid frog Xenopus laevis, and two copies in zebrafish (Danio rerio). For 22 of these genes, both zebrafish duplicates had orthologs in the pufferfish (Takifugu rubripes). For another 20 of these genes, we found only one pufferfish ortholog but in each case it was more closely related to one of the zebrafish duplicates than to the other. Forty-three pairs of duplicated genes map to 24 of the 25 zebrafish linkage groups but they are not randomly distributed; we identified 10 duplicated regions of the zebrafish genome that each contain between two and five sets of paralogous genes. These phylogeny and synteny data suggest that the common ancestor of zebrafish and pufferfish, a fish that gave rise to ∼22,000 species, experienced a large-scale gene or complete genome duplication event and that the pufferfish has lost many duplicates that the zebrafish has retained.[Supplemental material is available online at www.genome.org.]
Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
Authors: Li Li , Brunk Brian P. , Kissinger Jessica C. , Pape Deana , Tang Keliang , Cole Robert H. , Martin John , Wylie Todd , Dante Mike , Fogarty Steven J. , Howe Daniel K. , Liberator Paul , Diaz Carmen , Anderson Jennifer , White Michael , Jerome Maria E. , Johnson Emily A. , Radke Jay A. , Stoeckert Christian J. , Waterston Robert H. , Clifton Sandra W. , Roos David S. , Sibley L. David 
Published: March 2003

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%–20% represent putative homologs with a conservative cutoff of p < 10−9, thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.[The sequence data from this study have been submitted to dbEST division of GenBank under accession nos.:Toxoplasma gondii: BG657138–BG661027,BI921045–BI921090, BI946571–BI946588, BM003839–BM004582,BM039066– BM040645, BM131233–BM133172, BM174962–BM176879,BM188953–BM189923, BM271559–BM271694. Plasmodium falciparum:BI670521–BI670830, BI813842–BI816393, BI936022–BI936312,BM273300–BM276553. Sarcocystis neurona: BE574328, BE574347,BE574384, BE574386, BE574409, BE574465, BE574508, BE574543, BE574561,BE574633, BE574689, BE574694, BE574723, BE635418–BE636244,BE574288–BE574724, BF323572–BF324064, BM252128–BM253024,BM303125–BM305293. Eimeria tenella: AI755306–AI758088,AI759179–AI759181, AI759254–AI759304, AI759182–AI759253, AI759305–AI759387, AI759463–AI759546,AI759388–AI759462, AI759547–AI759621, BE027133– BE028807,BF023640–BF023711, BF023609–BF023639, BG235514–BG235880,BG413067–BG413336, BG466192–BG467045, BG515959–BG517044,BG560819–BG562379, BG724474–BG725148, BI895002–BI896127,BM305294–BM306971, BM321464–BM322026. Neospora caninum: BF248514–BF249435, BF716421–BF717094, BF823742,BF823805– BF823813, BF823743–BF824633, BG235070–BG235513.]
Alteration of Microtubule Dynamic Instability during Preprophase Band Formation Revealed by Yellow Fluorescent Protein–CLIP170 Microtubule Plus-End Labeling[W]
Authors: Dhonukshe Pankaj , Gadella Theodorus W. J. 
Published: March 2003

AbstractAt the onset of mitosis, plant cells form a microtubular preprophase band that defines the plane of cell division, but the mechanism of its formation remains a mystery. Here, we describe the use of mammalian yellow fluorescent protein–tagged CLIP170 to visualize the dynamic plus ends of plant microtubules in transfected cowpea protoplasts and in stably transformed and dividing tobacco Bright Yellow 2 cells. Using plus-end labeling, we observed dynamic instability in different microtubular conformations in live plant cells. The interphase plant microtubules grow at 5 μm/min, shrink at 20 μm/min, and display catastrophe and rescue frequencies of 0.02 and 0.08 events/s, respectively, exhibiting faster turnover than their mammalian counterparts. Strikingly, during preprophase band formation, the growth rate and catastrophe frequency of plant microtubules double, whereas the shrinkage rate and rescue frequency remain unchanged, making microtubules shorter and more dynamic. Using these novel insights and four-dimensional time-lapse imaging data, we propose a model that can explain the mechanism by which changes in microtubule dynamic instability drive the dramatic rearrangements of microtubules during preprophase band and spindle formation in plant cells.
Characterization of the Last Subunit of the Arabidopsis COP9 Signalosome: Implications for the Overall Structure and Origin of the Complex[W]
Authors: Serino Giovanna , Su Hongwen , Peng Zhaohua , Tsuge Tomohiko , Wei Ning , Gu Hongya , Deng Xing Wang 
Published: March 2003

AbstractThe COP9 signalosome (CSN) is an evolutionarily conserved protein complex that resembles the lid subcomplex of proteasomes. Through its ability to regulate specific proteasome-mediated protein degradation events, CSN controls multiple aspects of development. Here, we report the cloning and characterization of AtCSN2, the last uncharacterized CSN subunit from Arabidopsis. We show that the AtCSN2 gene corresponds to the previously identified FUS12 locus and that AtCSN2 copurifies with CSN, confirming that AtCSN2 is an integral component of CSN. AtCSN2 is not only able to interact with the SCFTIR1 subunit AtCUL1, which is partially responsible for the regulatory interaction between CSN and SCFTIR1, but also interacts with AtCUL3, suggesting that CSN is able to regulate the activity of other cullin-based E3 ligases through conserved interactions. Phylogenetic analysis indicated that the duplication and subsequent divergence events that led to the genes that encode CSN and lid subunits occurred before the divergence of unicellular and multicellular eukaryotic organisms and that the CSN subunits were more conserved than the lid subunits during evolution. Comparative analyses of the subunit interaction of CSN revealed a set of conserved subunit contacts and resulted in a model of CSN subunit topology, some aspects of which were substantiated by in vivo cross-link tests.
Roles of the Enantioselective Glutathione
S
-Transferases in Cleavage of β-Aryl Ether
Authors: Masai Eiji , Ichimura Atsushi , Sato Yusuke , Miyauchi Keisuke , Katayama Yoshihiro , Fukuda Masao 
Published: March 2003

ABSTRACT

Cleavage of the β-aryl ether linkage is the most important process in lignin degradation. Here we characterize the three tandemly located glutathione
S
-transferase (GST) genes,
ligF
,
ligE
, and
ligG
, from low-molecular-weight lignin-degrading
Sphingomonas paucimobilis
SYK-6, and we describe the actual roles of these genes in the β-aryl ether cleavage. Based on the identification of the reaction product by electrospray ionization-mass spectrometry, a model compound of β-aryl ether, α-(2-methoxyphenoxy)-β-hydroxypropiovanillone (MPHPV), was transformed by LigF or LigE to guaiacol and α-glutathionyl-β-hydroxypropiovanillone (GS-HPV). This result suggested that LigF and LigE catalyze the nucleophilic attack of glutathione on the carbon atom at the β position of MPHPV. High-pressure liquid chromatography-circular dichroism analysis indicated that LigF and LigE each attacked a different enantiomer of the racemic MPHPV preparation. The
ligG
gene product specifically catalyzed the elimination of glutathione from GS-HPV generated by the action of LigF. This reaction then produces an achiral compound, β-hydroxypropiovanillone, which is further degraded by this strain. Disruption of the
ligF
,
ligE
, and
ligG
genes in SYK-6 showed that
ligF
is essential to the degradation of one of the MPHPV enantiomers, and the alternative activities which metabolize the substrates of LigE and LigG are present in this strain.
The FecI Extracytoplasmic-Function Sigma Factor of
Escherichia coli
Interacts with the β′ Subunit of RNA Polymerase
Authors: Mahren Susanne , Braun Volkmar 
Published: March 2003

ABSTRACT

Transcription of the ferric citrate transport system of
Escherichia coli
K-12 is mediated by the extracytoplasmic-function (ECF) sigma factor FecI, which is activated by ferric citrate in the growth medium. By using a bacterial two-hybrid system, it was shown in vivo that FecI binds to the β′ subunit of RNA polymerase. The inactive mutant protein FecI(K155E) displayed reduced binding to β′, and small deletions along the entire FecI protein led to total impairment of β′ binding. In vitro, FecI was retained on Ni
2+
-nitrilotriacetic acid agarose loaded with a His-tagged β′
1-313
fragment and coeluted with β′
1-313
. Binding of FecI to β′ and β′
1-313
was enhanced by FecR
1-85
, which represents the cytoplasmic portion of the FecR protein that transmits the inducing signal across the cytoplasmic membrane. Interaction of FecR with FecI was demonstrated by showing that isolated FecR inhibited degradation of FecI by trypsin. This is the first demonstration of binding of an ECF sigma factor of the FecI type to the β′ subunit of RNA polymerase and of binding being enhanced by the protein that activates the ECF sigma factor.
The
Escherichia coli mazEF
Suicide Module Mediates Thymineless Death
Authors: Sat Boaz , Reches Myriam , Engelberg-Kulka Hanna 
Published: March 2003

ABSTRACT

In 1954, Cohen and Barner discovered that a thymine auxotrophic (
thyA
) mutant of
Escherichia coli
undergoes cell death in response to thymine starvation. This phenomenon, called thymineless death (TLD), has also been found in many other organisms, including prokaryotes and eukaryotes. Though TLD has been studied intensively, its molecular mechanism has not yet been explained. Previously we reported on the
E. coli mazEF
system, a regulatable chromosomal suicide module that can be triggered by various stress conditions. MazF is a stable toxin, and MazE is an unstable antitoxin. Here, we show that cell death that is mediated by the
mazEF
module can also be activated by thymine starvation. We found that TLD depends on
E. coli mazEF
and that under thymine starvation, the activity of the
mazEF
promoter P
2
is significantly reduced. Our results, which describe thymine starvation as a trigger for a built-in death program, have implications for programmed cell death in both prokaryotes and eukaryotes.
Identification of a Novel Membrane-Associated Gene Product That Suppresses Toxicity of a TrfA Peptide from Plasmid RK2 and Its Relationship to the DnaA Host Initiation Protein
Authors: Kim Peter D. , Banack Trevor , Lerman Daniel M. , Tracy Jeremiah C. , Camara Johanna Eltz , Crooke Elliot , Oliver Don , Firshein William 
Published: March 2003

ABSTRACTThe toxicity of a peptide derived from the amino-terminal portion of 33-kDa TrfA, one of the initiation proteins encoded by the broad-host-range plasmid RK2, was suppressed by a host protein related to DnaA, the initiation protein ofEscherichia coli. The newly identified 28.4-kDa protein, termed a DnaA paralog (Dp) because it is similar to a region of DnaA but likely has a different function in initiation of plasmid RK2 replication, interacts physically with the 33-kDa TrfA initiation protein, including the initiation-active monomeric form. The Dp has a cellular distribution similar to that of the 33-kDa TrfA initiation protein, being found primarily in the inner membrane fraction, with lesser amounts detected in the outer membrane fraction and almost none in the soluble fraction ofE. coli. Maintenance and inner membrane-associated replication of plasmid RK2 were enhanced in a Dp knockout strain and inhibited in strains containing extra copies of the Dp gene or in membrane extracts to which a tagged form of Dp was added. Recently, the Dp was independently shown to help prevent overinitiation inE. coliand was termed Hda (S. Kato and T. Katayama, EMBO J.20:4253-4262, 2001).