bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epinephrine‐supplemented local anesthetics for ear and nose surgery: Clinical use without complications in more than 10,000 surgical procedures
Authors: Häfner Hans‐Martin , Röcken Manfred , Breuninger Helmut 
Published: February 2005

Summary Introduction: Local anesthetics supplemented with epinephrine are generally regarded as contraindicated for surgical procedures involving the fingers, toes, penis, outer ear and the tip of the nose [1], but epinephrine is essential if automated tumescence local anesthesia (Auto‐TLA) is used. Materials and methods: Infiltration anesthesia supplemented with 1 : 200,000 epinephrine was used from 1985 – 1997 in our department, while Auto‐TLA supplemented with 1 : 1.000,000 epinephrine was introduced in 1997 for all surgical procedures involving the ear or nose. During this period, 10,201 patients underwent surgery at these locations.In addition, dermal blood flow was analyzed by acral photoplethysmography (APPG) and laser Doppler flowmetry (LDF) in the right ear lobe of five normal volunteers and during epinephrine supplemented Auto‐TLA. Results: Epinephrine‐induced complications were not observed in a single patient. Cosmetic skin flap surgery was performed in 4,953 of these patients. Even in patients with extended surgical procedures that took up to one to two hours and that included extensive skin flaps or skin grafts, we observed no increase in complications when compared to procedures performed either under general anesthesia or local anesthesia without epinephrine supplementation.Measuring blood perfusion of the earlobe showed a 69 % reduction of LDF and a 42 % reduction of arterial inflow (APPG) immediately following anesthesia. Conclusion: Epinephrine supplementation of local anesthetics does not block blood perfusion in the ear and did not induce organ, tissue or flap necrosis. Local anesthesia with epinephrine supplementation is therefore safe for acral areas such as the ear or nose. Despite the relatively small influence on blood perfusion, epinephrine supplementation results in a relatively bloodless operating field and longer effectiveness of local anesthesia. The relative absence of blood in the operating field of the ear and nose significantly reduces the duration of surgery and increases the healing rate, as less electrocautery is needed.
A Novel Mechanism for Desulfation of Mucin: Identification and Cloning of a Mucin-Desulfating Glycosidase (Sulfoglycosidase) from
Prevotella
Strain RS2
Authors: Rho Jung-hyun , Wright Damian P. , Christie David L. , Clinch Keith , Furneaux Richard H. , Roberton Anthony M. 
Published: February 2005

ABSTRACT

A novel enzyme which may be important in mucin degradation has been discovered in the mucin-utilizing anaerobe
Prevotella
strain RS2. This enzyme cleaves terminal 2-acetamido-2-deoxy-β-
d
-glucopyranoside 6-sulfate (6-SO
3
-GlcNAc) residues from sulfomucin and from the model substrate 4-nitrophenyl 2-acetamido-2-deoxy-β-
d
-glucopyranoside 6-sodium sulfate. The existence of this mucin-desulfating glycosidase (sulfoglycosidase) suggests an alternative mechanism by which this bacterium may desulfate sulfomucins, by glycosidic removal of a sulfated sugar from mucin oligosaccharide chains. Previously, mucin desulfation was thought to take place by the action of a specific desulfating enzyme, which then allowed glycosidases to remove desulfated sugar. Sulfate removal from sulfomucins is thought to be a rate-limiting step in mucin degradation by bacteria in the regions of the digestive tract with a significant bacterial flora. The sulfoglycosidase was induced by growth of the
Prevotella
strain on mucin and was purified 284-fold from periplasmic extracts. Tryptic digestion and sequencing of peptides from the 100-kDa protein enabled the sulfoglycosidase gene to be cloned and sequenced. Active recombinant enzyme was made in an
Escherichia coli
expression system. The sulfoglycosidase shows sequence similarity to hexosaminidases. The only other enzyme that has been shown to remove 6-SO
3
-GlcNAc from glycoside substrates is the human lysosomal enzyme β-
N
-acetylhexosaminidase A, point mutations in which cause the inheritable, lysosomal storage disorder Tay-Sachs disease. The human enzyme removes GlcNAc from glycoside substrates also, in contrast to the
Prevotella
enzyme, which acts on a nonsulfated substrate at a rate that is only 1% of the rate observed with a sulfated substrate.
Identification of Essential Amino Acid Residues of the NorM Na
+
/Multidrug Antiporter in
Vibrio parahaemolyticus
Authors: Otsuka Masato , Yasuda Makoto , Morita Yuji , Otsuka Chie , Tsuchiya Tomofusa , Omote Hiroshi , Moriyama Yoshinori 
Published: February 2005

ABSTRACT

NorM is a member of the multidrug and toxic compound extrusion (MATE) family and functions as a Na
+
/multidrug antiporter in
Vibrio parahaemolyticus
, although the underlying mechanism of the Na
+
/multidrug antiport is unknown. Acidic amino acid residues Asp32, Glu251, and Asp367 in the transmembrane region of NorM are conserved in one of the clusters of the MATE family. In this study, we investigated the role(s) of acidic amino acid residues Asp32, Glu251, and Asp367 in the transmembrane region of NorM by site-directed mutagenesis. Wild-type NorM and mutant proteins with amino acid replacements D32E (D32 to E), D32N, D32K, E251D, E251Q, D367A, D367E, D367N, and D367K were expressed and localized in the inner membrane of
Escherichia coli
KAM32 cells, while the mutant proteins with D32A, E251A, and E251K were not. Compared to cells with wild-type NorM, cells with the mutant NorM protein exhibited reduced resistance to kanamycin, norfloxacin, and ethidium bromide, but the NorM D367E mutant was more resistant to ethidium bromide. The NorM mutant D32E, D32N, D32K, D367A, and D367K cells lost the ability to extrude ethidium ions, which was Na
+
dependent, and the ability to move Na
+
, which was evoked by ethidium bromide. Both E251D and D367N mutants decreased Na
+
-dependent extrusion of ethidium ions, but ethidium bromide-evoked movement of Na
+
was retained. In contrast, D367E caused increased transport of ethidium ions and Na
+
. These results suggest that Asp32, Glu251, and Asp367 are involved in the Na
+
-dependent drug transport process.
Type III Secretion of the
Salmonella
Effector Protein SopE Is Mediated via an N-Terminal Amino Acid Signal and Not an mRNA Sequence
Authors: Karavolos M. H. , Wilson M. , Henderson J. , Lee J. J. , Khan C. M. A. 
Published: February 2005

ABSTRACT

Type III secretion systems (TTSS) are virulence-associated components of many gram-negative bacteria that translocate bacterial proteins directly from the bacterial cytoplasm into the host cell. The
Salmonella
translocated effector protein SopE has no consensus cleavable amino-terminal secretion sequence, and the mechanism leading to its secretion through the
Salmonella
pathogenicity island 1 (SPI-1) TTSS is still not fully understood. There is evidence from other bacteria which suggests that the TTSS signal may reside within the 5′ untranslated region (UTR) of the mRNA of secreted effectors. We investigated the role of the 5′ UTR in the SPI-1 TTSS-mediated secretion of SopE using promoter fusions and obtained data indicating that the mRNA sequence is not involved in the secretion process. To clarify the proteinaceous versus RNA nature of the signal, we constructed frameshift mutations in the amino-terminal region of SopE of
Salmonella enterica
serovar Typhimurium SL1344. Only constructs with the native amino acid sequence were secreted, highlighting the importance of the amino acid sequence versus the mRNA sequence for secretion. Additionally, we obtained frameshift mutation data suggesting that the first 15 amino acids are important for secretion of SopE independent of the presence of the chaperone binding site. These data shed light on the nature of the signal for SopE secretion and highlight the importance of the amino-terminal amino acids for correct targeting and secretion of SopE via the SPI-1-encoded TTSS during host cell invasion.
Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species
Authors: Fuhrer Tobias , Fischer Eliane , Sauer Uwe 
Published: February 2005

ABSTRACT

The structurally conserved and ubiquitous pathways of central carbon metabolism provide building blocks and cofactors for the biosynthesis of cellular macromolecules. The relative uses of pathways and reactions, however, vary widely among species and depend upon conditions, and some are not used at all. Here we identify the network topology of glucose metabolism and its in vivo operation by quantification of intracellular carbon fluxes from
13
C tracer experiments. Specifically, we investigated
Agrobacterium tumefaciens
, two pseudomonads,
Sinorhizobium meliloti
,
Rhodobacter sphaeroides
,
Zymomonas mobilis
, and
Paracoccus versutus
, which grow on glucose as the sole carbon source, represent fundamentally different metabolic lifestyles (aerobic, anaerobic, photoheterotrophic, and chemoheterotrophic), and are phylogenetically distinct (firmicutes, γ-proteobacteria, and α-proteobacteria). Compared to those of the model bacteria
Escherichia coli
and
Bacillus subtilis
, metabolisms of the investigated species differed significantly in several respects: (i) the Entner-Doudoroff pathway was the almost exclusive catabolic route; (ii) the pentose phosphate pathway exhibited exclusively biosynthetic functions, in many cases also requiring flux through the nonoxidative branch; (iii) all aerobes exhibited fully respiratory metabolism without significant overflow metabolism; and (iv) all aerobes used the pyruvate bypass of the malate dehydrogenase reaction to a significant extent. Exclusively,
Pseudomonas fluorescens
converted most glucose extracellularly to gluconate and 2-ketogluconate. Overall, the results suggest that metabolic data from model species with extensive industrial and laboratory history are not representative of microbial metabolism, at least not quantitatively.
Genome-Wide Analysis of the General Stress Response Network inEscherichia coli: σS-Dependent Genes, Promoters, and Sigma Factor Selectivity
Authors: Weber Harald , Polen Tino , Heuveling Johanna , Wendisch Volker F. , Hengge Regine 
Published: February 2005

ABSTRACTThe σS(or RpoS) subunit of RNA polymerase is the master regulator of the general stress response inEscherichia coli. While nearly absent in rapidly growing cells, σSis strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of theE. coligenes are under direct or indirect control of σSand that σSshould be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a σSconsensus promoter in silico. Moreover, our results suggest that σS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect σSand/or σ70selectivity of many promoters. These observations indicate that certain modules of the σS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with σ70RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.
Cupin-Type Phosphoglucose Isomerases (Cupin-PGIs) Constitute a Novel Metal-Dependent PGI Family Representing a Convergent Line of PGI Evolution
Authors: Hansen Thomas , Schlichting Bettina , Felgendreher Martina , Schönheit Peter 
Published: February 2005

ABSTRACT

Cupin-type phosphoglucose isomerases (cPGIs) were identified in some archaeal and bacterial genomes and the respective coding function of
cpgi
's from the euryarchaeota
Archaeoglobus fulgidus
and
Methanosarcina mazei
, as well as the bacteria
Salmonella enterica
serovar Typhimurium and
Ensifer meliloti
, was proven by functional overexpression. These cPGIs and the cPGIs from
Pyrococcus
and
Thermococcus
spp. represent the cPGI family and were compared with respect to kinetic, inhibitory, thermophilic, and metal-binding properties. cPGIs showed a high specificity for the substrates fructose-6-phosphate and glucose-6-phosphate and were inhibited by millimolar concentrations of sorbitol-6-phosphate, erythrose-4-phosphate, and 6-phosphogluconate. Treatment of cPGIs with EDTA resulted in a complete loss of catalytic activity, which could be regained by the addition of some divalent cations, most effectively by Fe
2+
and Ni
2+
, indicating a metal dependence of cPGI activity. The motifs TX
3
PX
3
GXEX
3
TXGHXHX
6-11
EXY and PPX
3
HX
3
N were deduced as the two signature patterns of the novel cPGI family. Phylogenetic analysis suggests lateral gene transfer for the bacterial cPGIs from euryarchaeota.
GenotypingMycobacterium ulceransandMycobacterium marinumby Using Mycobacterial Interspersed Repetitive Units
Authors: Stragier Pieter , Ablordey Anthony , Meyers Wayne M. , Portaels Françoise 
Published: February 2005

ABSTRACTA novel category of variable tandem repeats (VNTR) called mycobacterial interspersed repetitive units (MIRUs) has been identified forMycobacterium ulcerans(n= 39),M. marinum(n= 27), and one related organism. Fifteen MIRU loci were identified in the genome ofM. marinumand were used to genotypeM. ulcerans,M. marinum, and anM. marinum-like organism that is considered a possible missing link betweenM. marinumandM. ulcerans. Seven MIRU loci were polymorphic, and locus-specific PCRs for four of these loci differentiated sevenM. ulceransgenotypes, fourM. marinumgenotypes, and a unique genotype for the missing link organism. The sevenM. ulceransgenotypes were related to six different geographic origins of isolates. All isolates from West and Central Africa, including old and recent isolates, belonged to the same genotype, emphasizing the great spatiotemporal homogeneity among African isolates. Unlike theM. ulceransgenotypes, the fourM. marinumgenotypes could not be clearly related to the geographic origins of the isolates. According to MIRU-VNTR typing, allM. ulceransandM. marinumisolates of American origin were closely related, suggesting a common American ancestor for these two pathogenic species on the American continents. MIRU typing has significant potential value for discriminating between reoccurrence and reinfection forM. ulceransdisease.
Additional Determinants within
Escherichia coli
FNR Activating Region 1 and RNA Polymerase α Subunit Required for Transcription Activation
Authors: Weber K. Derek , Vincent Owen D. , Kiley Patricia J. 
Published: February 2005

ABSTRACT

The global anaerobic regulator FNR is a DNA binding protein that activates transcription of genes required for anaerobic metabolism in
Escherichia coli
through interactions with RNA polymerase (RNAP). Alanine-scanning mutagenesis of FNR amino acid residues 181 to 193 of FNR was utilized to determine which amino acid side chains are required for transcription of both class II and class I promoters. In vivo assays of FNR function demonstrated that a core of residues (F181, R184, S187, and R189) was required for efficient activation of class II promoters, while at a class I promoter, FF(−61.5), only S187 and R189 were critical for FNR activation. Site-directed mutagenesis of positions 184, 187, and 189 revealed that the positive charge contributes to the function of the side chain at positions 184 and 189 while the serine hydroxyl is critical for the function of position 187. Subsequent analysis of the carboxy-terminal domain of the α subunit (αCTD) of RNAP, using an alanine library in single copy, revealed that in addition to previously characterized side chains (D305, R317, and L318), E286 and E288 contributed to FNR activation of both class II and class I promoters, suggesting that αCTD region 285 to 288 also participates in activation by FNR. In conclusion, this study demonstrates that multiple side chains within region 181 to 192 are required for FNR activation and the surface of αCTD required for FNR activation is more extensive than previously observed.
Comparative Study of Class 1 Integron andVibrio choleraeSuperintegron Integrase Activities
Authors: Biskri Latefa , Bouvier Marie , Guérout Anne-Marie , Boisnard Stéphanie , Mazel Didier 
Published: February 2005

ABSTRACTSuperintegrons (SIs) and multiresistant integrons (MRIs) have two main structural differences: (i) the SI platform is sedentary, while the MRI platform is commonly associated with mobile DNA elements and (ii) the recombination sites (attC) of SI gene cassette clusters are highly homogeneous, while those of MRI cassette arrays are highly variable in length and sequence. In order to determine if the latter difference was correlated with a dissimilarity in the recombination activities, we conducted a comparative study of the integron integrases of the class 1 MRI (IntI1) and theVibrio choleraeSI (VchIntIA). We developed two assays that allowed us to independently measure the frequencies of cassette deletion and integration at the cognateattIsites. We demonstrated that the range ofattCsites efficiently recombined by VchIntIA is narrower than the range ofattCsites efficiently recombined by IntI1. Introduction of mutations into theV. choleraerepeats (VCRs), theattCsites of theV. choleraeSI cassettes, allowed us to map positions that affected the VchIntIA and IntI1 activities to different extents. Using a cointegration assay, we established that inE. coli,attI1-×-VCR recombination catalyzed by IntI1 was 2,600-fold more efficient thanattIVch-×-VCR recombination catalyzed by VchIntIA. We performed the same experiments inV. choleraeand established that theattIVch-×-VCR recombination catalyzed by VchIntIA was 2,000-fold greater than the recombination measured inE. coli. Taken together, our results indicate that in theV. choleraeSI, the substrate recognition and recombination reactions mediated by VchIntIA might differ from the class 1 MRI paradigm.
Evolution of Genomic Content in the Stepwise Emergence ofEscherichia coliO157:H7
Authors: Wick Lukas M. , Qi Weihong , Lacher David W. , Whittam Thomas S. 
Published: February 2005

ABSTRACTGenome comparisons have demonstrated that dramatic genetic change often underlies the emergence of new bacterial pathogens. Evolutionary analysis ofEscherichia coliO157:H7, a pathogen that has emerged as a worldwide public health threat in the past two decades, has posited that this toxin-producing pathogen evolved in a series of steps from O55:H7, a recent ancestor of a nontoxigenic pathogenic clone associated with infantile diarrhea. We used comparative genomic hybridization with 50-mer oligonucleotide microarrays containing probes from both pathogenic and nonpathogenic genomes to infer when genes were acquired and lost. Many ancillary virulence genes identified in the O157 genome were already present in an O55:H7-like progenitor, with 27 of 33 genomic islands of >5 kb and specific for O157:H7 (O islands) that were acquired intact before the split from this immediate ancestor. Most (85%) of variably absent or present genes are part of prophages or phage-like elements. Divergence in gene content among these closely related strains was ∼140 times greater than divergence at the nucleotide sequence level. A >100-kb region around the O-antigen gene cluster contained highly divergent sequences and also appears to be duplicated in its entirety in one lineage, suggesting that the whole region was cotransferred in the antigenic shift from O55 to O157. The β-glucuronidase-positive O157 variants, although phylogenetically closest to the Sakai strain, were divergent for multiple adherence factors. These observations suggest that, in addition to gains and losses of phage elements, O157:H7 genomes are rapidly diverging and radiating into new niches as the pathogen disseminates.
Crystal Structures of the BlaI Repressor from
Staphylococcus aureus
and Its Complex with DNA: Insights into Transcriptional Regulation of the
bla
and
mec
Operons
Authors: Safo Martin K. , Zhao Qixun , Ko Tzu-Ping , Musayev Faik N. , Robinson Howard , Scarsdale Neel , Wang Andrew H.-J. , Archer Gordon L. 
Published: February 2005

ABSTRACT

The 14-kDa BlaI protein represses the transcription of
blaZ
, the gene encoding β-lactamase. It is homologous to MecI, which regulates the expression of
mecA
, the gene encoding the penicillin binding protein PBP2a. These genes mediate resistance to β-lactam antibiotics in staphylococci. Both repressors can bind either
bla
or
mec
DNA promoter-operator sequences. Regulated resistance genes are activated via receptor-mediated cleavage of the repressors. Cleavage is induced when β-lactam antibiotics bind the extramembrane sensor of the sensor-transducer signaling molecules, BlaR1 or MecR1. The crystal structures of BlaI from
Staphylococcus aureus
, both in free form and in complex with 32 bp of DNA of the
mec
operator, have been determined to 2.0- and 2.7-Å resolutions, respectively. The structure of MecI, also in free form and in complex with the
bla
operator, has been previously reported. Both repressors form homodimers, with each monomer composed of an N-terminal DNA binding domain of winged helix-turn-helix topology and a C-terminal dimerization domain. The structure of BlaI in complex with the
mec
operator shows a protein-DNA interface that is conserved between both
mec
and
bla
targets. The recognition helix α3 interacts specifically with the conserved TACA/TGTA DNA binding motif. BlaI and, probably, MecI dimers bind to opposite faces of the
mec
DNA double helix in an up-and-down arrangement, whereas MecI and, probably, BlaI dimers bind to the same DNA face of
bla
promoter-operator DNA. This is due to the different spacing of
mec
and
bla
DNA binding sites. Furthermore, the flexibility of the dimeric proteins may make the C-terminal proteolytic cleavage site more accessible when the repressors are bound to DNA than when they are in solution, suggesting that the induction cascade involves bound rather than free repressor.
Alexander of Aphrodisias on Universals: Two Problematic Texts
Authors:   Sharples
Published: February 2005

AbstractTwo texts that raise problems for Alexander of Aphrodisias' theory of universals are examined. De anima 90.2-8 appears to suggest that universals are dependent on thought for their existence; this raises questions about the status both of universals and of forms. It is suggested that the passage is best interpreted as indicating that universals are dependent on thought only for their being recognised as universals. The last sentence of Quaestio 1.11 seems to assert that if the universal did not exist no individual would exist, thereby contradicting Alexander's position elsewhere. This seems to be a slip resulting from the fact that species with only one member are the exception rather than the rule.