bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular cloning and analysis of cDNA sequences for two ribosomal proteins from Artemia
Authors: MAASSEN J. Antonie , SCHOP Enno N. , BRANDS Jolanda H. G. M. , VAN HEMERT Formijn J. , LENSTRA Johannes A. , MÖLLER Wim 
Published: March 2005

The large subunit of eukaryotic ribosomes contains acidic phosphoproteins which are related to L7/L12 from Escherichia coli. In the brine shrimp Artemia these proteins are designated eL12 and eL12′. We have isolated cDNA clones for these proteins from a cDNA bank that was constructed by the use of size‐fractionated poly(A)‐rich RNA (8–10S fraction) from Artemia and a synthetic oligonucleotide as primer. Clones containing DNA sequences coding for eL12 and eL12′ were characterized by hybrid‐selected translation and DNA sequencing. The proteins eL12 and eL12′ share an identical peptide of 22 amino acids at their carboxy termini whereas the remaining part of the protein shows little sequence homology. The nucleotide sequences show a different codon use for the amino acids in the common carboxy terminus, thereby excluding a common exon coding for this part of both proteins. Despite the differences in amino acid sequence in the major part of eL 12 and eL 12′ the proteins have a considerable degree of homology on the basis of the distribution of hydrophobic and hydrophilic amino acids over the polypeptide chains, in agreement with a related folding and function of both proteins.Relative levels of mRNA coding for eL12, eL12′ and elongation factor 1α were determined during the development of Artemia from a dormant cyst to a nauplius. The data show a coordinate expression of the genes for EF‐1 α and both ribosomal proteins, excluding a differential expression of the genes for these related ribosomal proteins during embryogenesis.Analysis of the gene copy number for eL 12 and eL 12′ indicates the presence of a few genes for each protein.
Hepatic carbamoyl phosphate metabolism
Authors: PAUSCH Jürgen , RASENACK Jens , HÄUSSINGER Dieter , GEROK Wolfgang 
Published: March 2005

1. The interrelationship between the two carbamoyl phosphate pools in intact hepatocytes and intact liver was studied with respect to de novo pyrimidine synthesis by use of selective inhibitors of the mitochonodiral and the cytosolic carbamoyl‐phosphate synthetase.2. Inhibition of mitochondrial carbamoyl phosphate synthesis by 4‐pentenoate was without effect on galactosamine‐stimulated pyrimidine synthesis. Conditions favouring mitochondrial carbamoyl phosphate accumulation, like excess ammonium ions or L‐norvaline, led to an increase in pyrimidine synthesis bypassing the feedback inhibition of cytosolic carbamoyl‐phosphate synthetase by UTP.3. A stimulation of pyrimidine synthesis was not observed when the carbamoyl phosphate accumulation was due to aspartate deficiency in the presence of aminooxyacetate. The full response of pyrimidine synthesis to excess ammonium ions was restored, even in the presence of aminooxyacetate, when aspartate was substituted. This is explained by an inhibition of aspartate carbamoyltransferase flux [in view of the Km (aspartate = 0.7 mmol/1) of this enzyme] resulting from a 90% decrease in aspartate tissue levels.4. Acivicin, the inhibitor of cytosolic carbamoyl‐phosphate synthetase, completely abolished the galactosamine‐induced stimulation of pyrimidine synthesis, but was without effect on the stimulation of pyrimidine synthesis by ammonium ions and L‐norvaline.5. It is concluded that experimental changes in mitochondrial carbamoyl phosphate content exert effects on de novo pyrimidine synthesis; however, it is considered unlikely that relevant amounts of mitochondrial carbamoyl phosphate are used for pyrimidine synthesis under physiological conditions. In addition the data point to a potential regulatory role of aspartate in hepatic pyrimidine synthesis.
Activation of protein kinase isozymes by cyclic nucleotide analogs used singly or in combination
Authors: ØGREID Dagfinn , EKANGER Roald , SUVA Robert H. , MILLER Jon P. , STURM Priscilla , CORBIN Jackie D. , DØSKELAND Stein Ove 
Published: March 2005

104 cAMP analogs, most of them modified in the adenine moiety, were tested as activators of cAMP‐dependent protein kinase I (from rabbit or rat skeletal muscle) and kinase II (from bovine heart or rat skeletal muscle).When tested singly, only 2‐phenyl‐1, N6‐etheno‐cAMP showed a considerably (sevenfold) higher potency as an activator of kinase II than of kinase I. Analogs containing an 8‐amino modification preferentially activated kinase I, some being more than 10‐fold more potent as activators of kinase I than kinase II.When two analogs were combined, the concentration of one (complementary) analog required to half‐maximally activate each isozyme was determined in the presence of a fixed concentration of another (priming) analog. Analogs tested in combination had been analyzed for their affinity for the intrasubunit binding sites (A, B) of isozyme I and II. The degree to which complementary analogs preferentially activated one isozyme was plotted against the mean site selectivity, i.e. (affinity A/B isozyme I · affinity A/B isozyme II)1 /2. This plot produced a straight line, the slope of which reflected the ability of the priming analog to discriminate homologous sites on the isozymes. This means that the isozyme discriminating power of an analog pair can be quantitatively predicted from the affinity of the analogs for site A and B of the two enzymes. It also means that a systematic analysis of those features of analogs imparting a high mean site selectivity or the ability to discriminate between homologous isozyme sites will facilitate the synthesis of new even more isozyme‐selective analogs.
Evidence for two oxygen‐linked binding sites for polyanions in dromedary hemoglobin
Authors: AMICONI Gino , BERTOLLINI Alberto , BELLELLI Andrea , COLETTA Massimo , CONDÒ Saverio G. , BRUNORI Maurizio 
Published: March 2005

The functional properties of dromedary hemoglobin have been studied as a function of chloride, polyphosphates and pH and compared with those of human hemoglobin. The two proteins have the same amino acid residues at the anion‐binding sites as well as at the level of the groups responsible for the alkaline Bohr effect. Analysis of the experimental data reveals that: (a) intrinsic oxygen affinity and the Bohr effect are very similar for the two proteins; (b) the association equilibrium constants of chloride are substantially higher in the dromedary system, both in the unligated and ligated state; (c) two polyanion‐binding sites occur in dromedary oxy and deoxyhemoglobin; (d) association constants of polyphosphates for the higher‐affinity binding site (probably in the cavity between β chains) are comparable for the two proteins under physiological conditions; association constants for the second binding site in dromedary hemoglobin are not affected by pH changes; (e) the dependence of oxygen affinity in dromedary hemoglobin upon chloride concentration is complex, this anion at relatively low concentrations reverses the effect of millimolar polyphosphate; (f) both in stopped‐flow and flash photolysis experiments the kinetic behaviour of dromedary hemoglobin is consistent with the equilibrium results.The pronounced sensitivity to solvent composition of the functional properties of dromedary hemoglobin even in the oxy state stresses the potential relevance of this conformation for regulating the oxygen transport in vivo.
Insulin receptors and bioresponses in a human liver cell line (Hep G‐2)
Authors: PODSKALNY Judith M. , TAKEDA Shigemasa , SILVERMAN Robert E. , TRAN Dien , CARPENTIER Jean‐Louis , ORCI Lelio , GORDEN Phillip 
Published: March 2005

A newly developed human hepatoma cell line, designated Hep G‐2, expresses high‐affinity insulin receptors meeting all the expected criteria for classic insulin receptors. 125I‐insulin binding is time‐dependent and temperature‐dependent and unlabeled insulin competes for the labeled hormone with a half‐maximal displacement of 1–3 ng/ml. This indicates a Kd of about 10−10 M. Since Scatchard analysis of the binding data results in a curvilinear plot and unlabeled insulin accelerates the dissociation of bound hormone, these receptors exhibit the negative cooperative interactions characteristic of insulin receptors in many other cell and tissue types. Proinsulin and des(Ala, Asp)‐insulin compete for 125I‐insulin binding with 4% and 2%, respectively, of the potency of insulin. Anti‐(insulin receptor) antibody competes fully for insulin binding. The two insulin‐like growth factors, multiplication‐stimulating activity and IGF‐I are 2% as potent as insulin against the Hep G‐2 insulin receptor. Furthermore, Hep G‐2 cells respond to insulin in several bioassays. Glucose uptake, glycogen synthase, uridine incorporation into RNA and acetate incorporation into lipid are all stimulated to varying degrees by physiological concentrations of insulin. In addition, these cells ‘down‐regulate’ their insulin receptor, internalize 125I‐insulin and degrade insulin in a manner similar to freshly isolated rodent hepatocytes.This is the first available human liver cell line in permanent culture in which both insulin receptors and biological responses have been carefully examined.
Novel phosphonoglycosphingolipids containing pyruvylated galactose from the nervous system of Aplysia kurodai
Authors: ARAKI Shigeko , ABE Sachiko , SATAKE Mei , HAYASHI Akira , KON Kazuo , ANDO Susumu 
Published: March 2005

We have reported the existence of a phosphonoglycosphingolipid containing a pyruvylated galactose, FGL‐IIb, in nerve fibers of Aplysia kurodai (Araki, S., Abe, S., Ando, S., Kon, K., Fujiwara, N. & Satake, M. (1989) J. Biol. Chem. 264, 19 922–19 927).We have now isolated two other pyruvylated galactose‐containing phosphonoglycosphingolipids, named FGL‐V and FGL‐IIa, from the nervous tissue of Aplysia, and characterized them as [3,4‐O‐(S‐1‐carboxy‐ethylidene)]Galβ1 → 3GalNAcα1 → 3[6′‐O‐(2‐aminoethylphosphonyl)Galα1 → 2] (2‐aminoethylphosphonyl → 6) Galβ1 → 4Glcβ1 → 1 ceramide and [3,4,O‐(S‐1‐carboxyethylidene)]Galβ1 → 3GalNAc α1 → 3[6′‐O‐(2‐aminoethylphosphonyl)Galα1 → 2]Galβ1 → 4Glcβ11 → ceramide, respectively.Their major aliphatic components are palmitic acid, octadeca‐4‐sphingenine and anteisononadeca‐4‐sphingenine.Thus, the nervous system of Aplysia contains several pyruvylated phosphonoglycolipids.
Pilot study of a breath test for volatile organic compounds associated with oral malodor: evidence for the role of oxidative stress
Authors: Phillips M , Cataneo RN , Greenberg J , Munawar MI , Nachnani S , Samtani S 
Published: March 2005

Background:  We performed a pilot study of a new method to identify the volatile organic compounds (VOCs) in breath associated with oral malodor, using gas chromatography and mass spectroscopy (GC/MS).Methods:  Oral cavity breath was collected from seven patients with oral malodor. Breath samples (150 ml) were concentrated onto sorbent traps and analyzed by GC/MS.Results:  Organoleptic scores ranged from 3.0 to 4.0 (mean = 3.3) on a scale of 0–5. Twenty‐four of 30 (80.0%) of the most abundant oral malodor volatile organic compounds (OMVOCs) were alkanes and methylated alkanes. These VOCs are products of oxidative stress, generated by lipid peroxidation of polyunsaturated fatty acids in cell membranes.Conclusions:  Increased oxidative stress in the oral cavity of patients with oral malodor may account for the increased risk of atherosclerosis, coronary heart disease and stroke associated with periodontal disease. The breath test for OMVOCs could potentially provide an objective new test for the assessment of oral malodor.
Quantitative detection of volatile sulfur compound‐ producing microorganisms in oral specimens using real‐time PCR
Authors: Kato H , Yoshida A , Awano S , Ansai T , Takehara T 
Published: March 2005

Objective:  It is well‐known that some periodontopathic bacteria, especially Porphyromonas gingivalis, Fusobacterium nucleatum, Tannerella forsythia (formerly Bacteroides forsythus or Tan. forsythensis), and Treponema denticola, actively produce volatile sulfur compounds (VSCs), such as H2S and CH3SH. We previously reported a qualitative relationship between periodontopathic bacteria and VSCs; however, a quantitative analysis of periodontopathic bacteria in oral specimens is required for further characterization of the relationship between oral bacteria and VSCs. In this study, we report a real‐time polymerase chain reaction (PCR) method for the quantitative analysis of VSC‐producing bacteria in oral specimens.Subjects and methods:  Specimens were collected from 22 patients who visited the Preventive Dentistry and Breath Odor Clinic of Kyushu Dental College. A real‐time PCR assay using the TaqMan system, based on the 5′–3′ exonuclease activity of Taq polymerase, was employed for the quantitative analysis of periodontopathic bacteria that produce VSCs.Results:  Using real‐time PCR, we performed a quantitative analysis of P. gingivalis, F. nucleatum, Tan. forsythia, and T. denticola in the saliva, on the tongue coat, and in the subgingival plaque of patients with oral malodor.Conclusion:  Real‐time PCR using the TaqMan system can be used for the quantitative analysis of VSC‐producing oral bacteria.
Biosynthesis of Auxin by the Gram-Positive PhytopathogenRhodococcus fasciansIs Controlled by Compounds Specific to Infected Plant Tissues
Authors: Vandeputte Olivier , Öden Sevgi , Mol Adeline , Vereecke Danny , Goethals Koen , El Jaziri Mondher , Prinsen Els 
Published: March 2005

ABSTRACTThe role and metabolism of indole-3-acetic acid in gram-negative bacteria is well documented, but little is known about indole-3-acetic acid biosynthesis and regulation in gram-positive bacteria. The phytopathogenRhodococcus fascians, a gram-positive organism, incites diverse developmental alterations, such as leafy galls, on a wide range of plants. Phenotypic analysis of a leafy gall suggests that auxin may play an important role in the development of the symptoms. We show here for the first time thatR. fasciansproduces and secretes the auxin indole-3-acetic acid. Interestingly, whereas noninfected-tobacco extracts have no effect, indole-3-acetic acid synthesis is highly induced in the presence of infected-tobacco extracts when tryptophan is not limiting. Indole-3-acetic acid production by a plasmid-free strain shows that the biosynthetic genes are located on the bacterial chromosome, although plasmid-encoded genes contribute to the kinetics and regulation of indole-3-acetic acid biosynthesis. The indole-3-acetic acid intermediates present in bacterial cells and secreted into the growth media show that the main biosynthetic route used byR. fasciansis the indole-3-pyruvic acid pathway with a possible rate-limiting role for indole-3-ethanol. The relationship between indole-3-acetic acid production and the symptoms induced byR. fasciansis discussed.
Acquisition of Resistance to Extended-Spectrum Cephalosporins by
Salmonella enterica
subsp.
enterica
Serovar Newport and
Escherichia coli
in the Turkey Poult Intestinal Tract
Authors: Poppe C. , Martin L. C. , Gyles C. L. , Reid-Smith R. , Boerlin P. , McEwen S. A. , Prescott J. F. , Forward K. R. 
Published: March 2005

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Newport resistant to the extended-spectrum cephalosporins (ESCs) and other antimicrobials causes septicemic salmonellosis in humans and animals and is increasingly isolated from humans, animals, foods, and environmental sources. Mechanisms whereby serovar Newport bacteria become resistant to ESCs and other classes of antimicrobials while inhabiting the intestinal tract are not well understood. The present study shows that 25.3% of serovar Newport strains isolated from the turkey poult intestinal tract after the animals were dosed with
Escherichia coli
harboring a large conjugative plasmid encoding the CMY-2 β-lactamase and other drug resistance determinants acquired the plasmid and its associated drug resistance genes. The conjugative plasmid containing the
cmy-2
gene was transferred not only from the donor
E. coli
to
Salmonella
serovar Newport but also to another
E. coli
serotype present in the intestinal tract. Laboratory studies showed that the plasmid could be readily transferred between serovar Newport and
E. coli
intestinal isolates. Administration of a single dose of ceftiofur, used to prevent septicemic colibacillosis, to 1-day-old turkeys did not result in the isolation of ceftiofur-resistant
E. coli
or
Salmonella
serovar Newport. There was a remarkable association between serotype, drug resistance, and plasmid profile among the
E. coli
strains isolated from the poults. This study shows that
Salmonella
serovar Newport can become resistant to ESCs and other antibiotics by acquiring a conjugative drug resistance plasmid from
E. coli
in the intestines.
Influence of Starvation on Potential Ammonia-Oxidizing Activity and
amoA
mRNA Levels of
Nitrosospira briensis
Authors: Bollmann Annette , Schmidt Ingo , Saunders Aaron M. , Nicolaisen Mette H. 
Published: March 2005

ABSTRACT

The effect of short-term ammonia starvation on
Nitrosospira briensis
was investigated. The ammonia-oxidizing activity was determined in a concentrated cell suspension with a NO
x
biosensor. The apparent half-saturation constant [

K
m(app)

] value of the NH
3
oxidation of
N. briensis
was 3 μM NH
3
for cultures grown both in continuous and batch cultures as determined by a NO
x
biosensor. Cells grown on the wall of the vessel had a lower

K
m(app)

value of 1.8 μM NH
3
. Nonstarving cultures of
N. briensis
showed potential ammonia-oxidizing activities of between 200 to 250 μM N h
−1
, and this activity decreased only slowly during starvation up to 10 days. Within 10 min after the addition of fresh NH
4
+
, 100% activity was regained. Parallel with activity measurements,
amoA
mRNA and 16S rRNA were investigated. No changes were observed in the 16S rRNA, but a relative decrease of
amoA
mRNA was observed during the starvation period. During resuscitation, an increase in
amoA
mRNA expression was detected simultaneously. The patterns of the soluble protein fraction of a 2-week-starved culture of
N. briensis
showed only small differences in comparison to a nonstarved control. From these results we conclude that
N. briensis
cells remain in a state allowing fast recovery of ammonia-oxidizing activity after addition of NH
4
+
to a starved culture. Maintaining cells in this kind of active state could be the survival strategy of ammonia-oxidizing bacteria in nature under fluctuating NH
4
+
availability.
Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm
Authors: Toner Brandy , Fakra Sirine , Villalobos Mario , Warwick Tony , Sposito Garrison 
Published: March 2005

ABSTRACT

Pseudomonas putida
strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn
+2
[Mn
+2
(aq)
] by
P. putida
was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L
2,3
absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn
+2
(aq)
was removed from solution by
P. putida
and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.
Differential Activities of FourLactobacillus caseiPromoters during Bacterial Transit through the Gastrointestinal Tracts of Human-Microbiota-Associated Mice
Authors: Oozeer R. , Furet J. P. , Goupil-Feuillerat N. , Anba J. , Mengaud J. , Corthier G. 
Published: March 2005

ABSTRACTIn a previous study using fusion of the deregulated lactose promoterlacTp*and reporter genes, we suggested thatLactobacillus caseicould initiate de novo protein synthesis during intestinal transit. In order to confirm this finding and extend it to other promoters, we adopted a reverse transcriptase quantitative PCR (RT-QPCR) approach combined with a transcriptional fusion system consisting of luciferase genes under the control of four promoters (ccpA,dlt,ldh, andlacT*) fromL. caseiDN-114 001. Promoter expression was monitored during cell growth, and variable luciferase activities were detected. In 3-day cultures, all the genetically modified strains survived but without exhibiting luciferase activity. Luciferase mRNA levels determined by RT-QPCR analysis (RNA/CFU) were not significant. The cultures were administered to human-microbiota-associated mice, and the feces were collected 6 h later.L. caseipromoterslacTp* andldhp initiated mRNA synthesis during gastrointestinal transit. The promoters,ccpAp anddltp, exhibited no luciferase activity, nor was de novo-synthesized luciferase mRNA detected in the feces.L. caseiseems to adapt its physiology to the gastrointestinal tract environment by modulating promoter activities. The approach (fecal transcriptional analysis) described herein may, moreover, be of value in studying gene expression of transiting bacteria in human fecal specimens.
Histamine-Producing Pathway Encoded on an Unstable Plasmid in
Lactobacillus hilgardii
0006
Authors: Lucas Patrick M. , Wolken Wout A. M. , Claisse Olivier , Lolkema Juke S. , Lonvaud-Funel Aline 
Published: March 2005

ABSTRACT

Histamine production from histidine in fermented food products by lactic acid bacteria results in food spoilage and is harmful to consumers. We have isolated a histamine-producing lactic acid bacterium,
Lactobacillus hilgardii
strain IOEB 0006, which could retain or lose the ability to produce histamine depending on culture conditions. The
hdcA
gene, coding for the histidine decarboxylase of
L. hilgardii
IOEB 0006, was located on an 80-kb plasmid that proved to be unstable. Sequencing of the
hdcA
locus disclosed a four-gene cluster encoding the histidine decarboxylase, a protein of unknown function, a histidyl-tRNA synthetase, and a protein, which we named HdcP, showing similarities to integral membrane transporters driving substrate/product exchange. The gene coding for HdcP was cloned downstream of a sequence specifying a histidine tag and expressed in
Lactococcus lactis
. The recombinant HdcP could drive the uptake of histidine into the cell and the exchange of histidine and histamine. The combination of HdcP and the histidine decarboxylase forms a typical bacterial decarboxylation pathway that may generate metabolic energy or be involved in the acid stress response. Analyses of sequences present in databases suggest that the other two proteins have dispensable functions. These results describe for the first time the genes encoding a histamine-producing pathway and provide clues to the parsimonious distribution and the instability of histamine-producing lactic acid bacteria.