bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosylnicotinamide Kinase Domain of NadR Protein: Identification and Implications in NAD Biosynthesis
Authors: Kurnasov Oleg V. , Polanuyer Boris M. , Ananta Shubha , Sloutsky Roman , Tam Annie , Gerdes Svetlana Y. , Osterman Andrei L. 
Published: November 2002

ABSTRACTNAD is an indispensable redox cofactor in all organisms. Most of the genes required for NAD biosynthesis in various species are known. Ribosylnicotinamide kinase (RNK) was among the few unknown (missing) genes involved with NAD salvage and recycling pathways. Using a comparative genome analysis involving reconstruction of NAD metabolism from genomic data, we predicted and experimentally verified that bacterial RNK is encoded within the 3′ region of thenadRgene. Based on these results and previous data, the full-size multifunctional NadR protein (as inEscherichia coli) is composed of (i) an N-terminal DNA-binding domain involved in the transcriptional regulation of NAD biosynthesis, (ii) a central nicotinamide mononucleotide adenylyltransferase (NMNAT) domain, and (iii) a C-terminal RNK domain. The RNK and NMNAT enzymatic activities of recombinant NadR proteins fromSalmonella entericaserovar Typhimurium andHaemophilus influenzaewere quantitatively characterized. We propose a model for the complete salvage pathway from exogenousN-ribosylnicotinamide to NAD which involves the concerted action of the PnuC transporter and NRK, followed by the NMNAT activity of the NadR protein. Both thepnuCandnadRgenes were proven to be essential for the growth and survival ofH. influenzae, thus implicating them as potential narrow-spectrum drug targets.
Molecular Genetic Analysis of ICEF, an Integrative Conjugal Element That Is Present as a Repetitive Sequence in the Chromosome ofMycoplasma fermentansPG18
Authors: Calcutt Michael J. , Lewis Michelle S. , Wise Kim S. 
Published: November 2002

ABSTRACTMycoplasmagenomes contain compact gene sets that approach the minimal complement necessary for life and reflect multiple evolutionary instances of genomic reduction. Lateral gene transfer may play a critical role in shaping the mobile gene pool in these organisms, yet complex mobile elements have not been reported within this genus. We describe here a large (∼23-kb) genetic element with unique features that is present in four copies in theMycoplasma fermentansPG18 chromosome, accounting for approximately 8% of the genome. These novel elements, designated ICEF (integrative conjugal elements ofM. fermentans), resemble conjugative, self-transmissible integrating elements (constins) in that circular, nonreplicative extrachromosomal forms occur in which the left and right termini of the integrated element are juxtaposed and separated by a coupling sequence derived from direct repeats flanking chromosomal copies of ICEF as a result of target site duplication. ICEF contain multiple similarly oriented open reading frames (ORFs), of which some have homology to products of known conjugation genes but others have no known counterparts. Surprisingly, unlike other constins, ICEF lack homologs of known integrases, transposases, or recombinases, suggesting that a novel enzyme may be employed for integration-excision. Skewed distribution and varied sites of chromosomal integration amongM. fermentansisolates suggest a role for ICEF in promoting genomic and phenotypic variation in this species. Identification of homologs of terminal ICEF ORFs in two additional mycoplasma species indicates that ICEF is the prototype member of a family of ICE-related elements that may be widespread among pathogenic mycoplasmas infecting diverse vertebrate hosts.
Vancomycin Tolerance Induced by Erythromycin but Not by Loss ofvncRS,vex3, orpep27Function inStreptococcus pneumoniae
Authors: Robertson Gregory T. , Zhao Jingyong , Desai Bhushan V. , Coleman William H. , Nicas Thalia I. , Gilmour Raymond , Grinius Leo , Morrison Donald A. , Winkler Malcolm E. 
Published: November 2002

ABSTRACTVancomycin-tolerantStreptococcus pneumoniaeis a growing problem among drug-resistant human pathogens. Some vancomycin-tolerant pneumococci have been reported to carry mutations in loci encoding a two-component regulatory system designated VncRS or in a proximal ABC transporter, Vex. A model was advanced proposing that the tolerance phenotype resulted from the inability of avncSmutant to respond to the Vex-transported Pep27 “death peptide” signal and dephosphorylate VncR, thereby preventing relief of repression of autolytic and other cell death functions in response to antibiotics. To explore this hypothesis, we constructed mutations invncS,vncR,vex3, andpep27inS. pneumoniaestrain R6 and two additional genetic backgrounds. The lytic responses of the isogenic ΔvncS, Δvex3, ΔvncR, and Δpep27mutants, but not a ΔlytAstrain, to vancomycin were indistinguishable from that of the parent strain. ΔvncSstrains also failed to exhibit tolerance to vancomycin at various doses in multiple media and showed wild-type sensitivity to other classes of autolysis-inducing antibiotics. In contrast, addition of subinhibitory levels of the antibiotic erythromycin led to tolerance to vancomycin during late, but not early, exponential-phase growth in a ΔvncSstrain, in the parent strain R6, and in two other strains bearing erythromycin resistance markers, namely, a ΔvncRstrain and an unrelated ΔcomDstrain that is defective in competence-quorum sensing. Thus, this tolerance effect resulted from changes in cell growth or other erythromycin-dependent phenomena and not inactivation ofvncSper se. Consistent with these results, and in contrast to a previous report, we found that a synthetic form of Pep27 did not elicit lytic or nonlytic killing of pneumococci. Finally, microarray transcriptional analysis and β-galactosidase reporter assays revealed VncS-dependent regulation of thevex123gene cluster but did not support a role for VncRS in the regulation of autolytic or other putative cell death loci. Based on these findings, we propose that vancomycin tolerance inS. pneumoniaedoes not result from loss ofvncSfunction alone.
Collaborative Regulation ofEscherichia coliGlutamate-Dependent Acid Resistance by Two AraC-Like Regulators, GadX and GadW (YhiW)
Authors: Ma Zhuo , Richard Hope , Tucker Don L. , Conway Tyrrell , Foster John W. 
Published: November 2002

ABSTRACTAn important feature ofEscherichia colipathogenesis is an ability to withstand extremely acidic environments of pH 2 or lower. This acid resistance property contributes to the low infectious dose of pathogenicE. colispecies. One very efficientE. coliacid resistance system encompasses two isoforms of glutamate decarboxylase (gadAandgadB) and a putative glutamate:γ-amino butyric acid (GABA) antiporter (gadC). The system is subject to complex controls that vary with growth media, growth phase, and growth pH. Previous work has revealed that the system is controlled by two sigma factors, two negative regulators (cyclic AMP receptor protein [CRP] and H-NS), and an AraC-like regulator called GadX. Earlier evidence suggested that the GadX protein acts both as a positive and negative regulator of thegadAandgadBCgenes depending on environmental conditions. New data clarify this finding, revealing a collaborative regulation between GadX and another AraC-like regulator called GadW (previously YhiW). GadX and GadW are DNA binding proteins that form homodimers in vivo and are 42% homologous to each other. GadX activates expression ofgadAandgadBCat any pH, while GadW inhibits GadX-dependent activation. Regulation ofgadAandgadBCby either regulator requires an upstream, 20-bp GAD box sequence. Northern blot analysis further indicates that GadW represses expression ofgadX. The results suggest a control circuit whereby GadW interacts with both thegadAandgadXpromoters. GadW clearly repressesgadXand, in situations where GadX is missing, activatesgadAandgadBC.GadX, however, activates onlygadAandgadBCexpression. CRP also repressesgadXexpression. It does this primarily by repressing production of sigma S, the sigma factor responsible forgadXexpression. In fact, the acid induction ofgadAandgadBCobserved when rich-medium cultures enter stationary phase corresponds to the acid induction of sigma S production. These complex control circuits impose tight rein over expression of thegadAandgadBCsystem yet provide flexibility for inducing acid resistance under many conditions that presage acid stress.
Electrocatalysis of polyaniline formation by PbO2 in acetonitrile
Authors: Abaci Serdar , Pekmez Kadir , Pekmez Nuran , Yildiz Attila 
Published: November 2002

AbstractElectrocatalytic effects on electropolymerization of aniline were investigated. It was determined that surface catalysis by β‐PbO2 causes formation of higher amounts of polyaniline than catalysis by α‐PbO2 and Pb2+ ions. β‐PbO2 surfaces decreased the upper potential limit of aniline electropolymerization about 400 mV. The catalytic effect of PbO2 is highly dependent upon the crystal structure of PbO2. Dry conductivity values of polyaniline samples obtained under different conditions were also compared. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 599–605, 2003
Hydrolytic degradation studies on poly(phosphate ester)s
Authors: Narendran N. , Kishore K. 
Published: November 2002

AbstractEight poly(phosphate ester)s comprising five homopolymers (polymers I–V), two copolymers (polymers VI and VII), and one terpolymer (polymer VIII) were synthesized by interfacial polycondensation of phenyl phosphorodichloridate with various bisphenols. The polymers were characterized by spectroscopic techniques. The copolymer and terpolymer ratios were determined by 1H‐NMR spectroscopy. The molecular weights of the polymers were determined by end‐group analysis using 31P‐NMR spectroscopy. Accelerated hydrolytic degradation studies under alkali‐catalyzed conditions showed that the polymer from biphenol (polymer IV) is the most stable and the polymer from thiodiphenol (polymer V) is the least stable. The products of hydrolytic degradation were analyzed and a suitable mechanism for the degradation of the polymers proposed. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 626–631, 2003
Parameters affecting the chain extension and branching of PET in the melt state by polyepoxides
Authors: Dhavalikar R. , Xanthos M. 
Published: November 2002

AbstractThis article describes the chemical modification of polyethylene terephthalate (PET) with a variety of compounds containing reactive glycidyl group(s). Four different modifiers, namely, diglycidyl ether of bisphenol‐A (DGEBA), N,N′‐bis[3(carbo‐2′,3′‐epoxypropoxy) phenyl] pyromellitimide (BGPM), triglycidyl glycerol (TGG), and triglycidyl isocyanurate (TGIC) were compared for their reactivity toward PET in the melt phase. It was found that the presence of tertiary nitrogen in the structure of the epoxide modifiers plays the role of in‐built catalyst for their reaction with the end groups of PET. TGIC as a modifier was selected for the detailed investigation of the simultaneously occurring degradation and chain extension/branching reactions in a batch‐melt mixer. The reactions were followed by torque changes, analyzing the products for residual carboxyl content, and by determining insoluble content. It is shown that the rate of the reactive modification of PET melt by TGIC depends upon stoichiometry, temperature, rate of shear, and the chemical composition and the molecular weight (MW) of the PET resin. In general, the results indicate an increase in melt viscosity and insoluble content, whereas an overall decrease in carboxyl content occurs, as defined by the choice of mixing conditions and stoichiometry. Analysis of the batch kinetic data can be useful to define the process requirements for carrying out the reactive modification in continuous extrusion equipment. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 643–652, 2003
Fish and ostracod remains from the Santos Basin (Cretaceous to Recent), Brazil
Authors: Giles Miller C. , Richter Martha , Do Carmo Dermeval A. 
Published: November 2002

AbstractFor the first time, ichthyoliths are described from the Santos sedimentary basin, offshore southern Brazil. Isolated teeth, dermal scales and the first documented otoliths from Cretaceous (Albian) to Recent cuttings from five wells are described. The following groups are represented: Chondrichthyans: Triakidae, Carcharhinidae; Ginglymostomatidae: ?Ginglymostomasp., Lamnidae indet., Scyliorhinidae; Osteichthyans: Teleostei; Myctophiidae:Diaphusaff.splendidussp. complex,Diaphusspp.,Diaphuscf.garmani,Ceratoscopelusaff.warmingii; Sternoptychidae:Valenciennellus tripunctulatus, teeth of indeterminate Teleostei. The majority of these ichthyofossils represent extant forms, known to occur in the Atlantic Ocean, and are of potential value for stratigraphical correlations between oil‐yielding basins in the region. Ostracods are not well preserved but can be identified to generic level indicating marine environments. The ostracod faunas offer potential for intrabasinal correlation in the Eocene and Oligocene. Copyright © 2002 John Wiley & Sons, Ltd.
Reductionism and the search for structure–function relationships in antibody molecules
Authors: Van Regenmortel Marc H. V. 
Published: November 2002

AbstractOne of the claims of reductionism is that it can explain all the features of living systems by an analysis of their physico‐chemical constituents. Such a claim disregards the existence in biological systems of emergent properties that do not exist in their isolated components but which allow autonomous organisms to be directively organized in a self‐regulated and integrated manner. It is not possible to describe biological systems adequately without using functional language that is meaningless in the physical sciences. The description of biological functions is also an essential part of immunology and functional explanations are more useful than causal explanations also in this discipline. Since causality is not a relation between a material object and an event, the structure of an antibody cannot be the cause of its binding activity. When structure–function relationships are analysed, the search should be for correlations rather than for causal relations. Methods used to find correlations between the atomic structure of antibody binding sites and their binding activity are mostly based on mutagenesis studies. Since the effect of any mutation depends on the molecular context, it is usually very difficult to predict the effects of multiple mutations on antibody function. Our knowledge of the molecular basis of antigen–antibody recognition has led to the expectation that it may be possible to develop new vaccines using molecular design principles. Such unwarranted hopes arise because of a confusion between antigenicity and immunogenicity. Although knowledge of antibody structure is of little use in vaccine design, it may help to develop therapeutic inhibitors and antibodies effective in the passive immunotherapy of viral infection Copyright © 2002 John Wiley & Sons, Ltd.
An investigation into the interference rejection capability of a linear array in a wireless communications system
Authors: Durrani Salman , Bialkowski Marek E. 
Published: November 2002

AbstractThe suitable use of an array antenna at the base station of a wireless communications system can result in improvement in the signal‐to‐interference ratio (SIR). In general, the SIR is a function of the direction of arrival of the desired signal and depends on the configuration of the array, the number of elements, and their spacing. In this paper, we consider a uniform linear array antenna and study the effect of varying the number of its elements and inter‐element spacing on the SIR performance. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 445–449, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10634
A novel wideband antenna package design with a compact spatial‐notch filter for wireless applications
Authors: Yeo Junho , Mittra Raj 
Published: November 2002

AbstractThis paper presents a compact package, comprising a wideband antenna with a compact spatial‐notch filter, useful for RF applications requiring a high rate of data transfer. Fractal concepts are employed to help reduce the package to almost half the normal size, and to realize a much sharper band‐stop than would be possible with a conventional filter. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 455–460, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10637
An inverse problem of normal incidence TE plane‐wave scattering and the method of lines
Authors: Hooshyar M. A. 
Published: November 2002

AbstractThe direct and inverse problems of normally incident TE plane‐wave scattering by perfectly conducting cylindrical structures with arbitrary cross sections are considered. It is shown that application of the method of lines results in an efficient procedure for calculating the scattering amplitude and also for determining the shape of cylindrical structures if the electromagnetic scattering amplitude is given. To illustrate the procedure, some realistic numerical examples are presented. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 486–491, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10645
Broadband conical printed quadrifilar helical antenna with integrated feed network
Authors: Yang Shiwen , Tan Soon Hie , Gan Yeow Beng , See Chun Wee 
Published: November 2002

AbstractA new approach to designing a broadband printed quadrifilar helical antenna (PQHA) is presented. The printed wire is conical in shape, while the feed network is directly integrated underneath the antenna. The entire system is designed using Ansoft HFSS. Good agreement with the experimental results is obtained. The impedance and axial ratio bandwidth values are greater than 32.4% and 18.5%, respectively. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 491–493, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10646
A fast and practical approach to the determination of junction temperature and thermal resistance for BJT/HBT devices
Authors: Ooi Ban Leong , Chen Bo , Lin Fujiang , Kooi Pang Shyan , Hui Chi So 
Published: November 2002

AbstractA simple, robust, accurate method to extract the thermal resistance of BJT/HBT devices is proposed, which only needs the measured device DC I‐V characteristics at room temperature. No optimization is needed to extract the thermal resistance. The proposed method is verified using a variety of BJT/HBT devices. Compared to the measured results taken from both CW DC measurements and isothermal measurements, the extracted values using our method is in excellent agreement with the conventional method. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 499–502, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10648
Efficient multiwavelength generation of Brillouin/erbium fiber laser at 1600‐nm region
Authors: Harun S. W. , Tamchek N. , Poopalan P. , Ahmad H. 
Published: November 2002

AbstractAn efficient Brillouin/erbium fiber laser, which operates in the 1600‐nm (L‐band) region, is demonstrated for potential applications in future dense‐wavelength division multiplexing communication systems. The laser configuration consists of an L‐band EDFA (to enable L‐band amplification) where two 3‐dB couplers take a portion of the generated BEFL signal and re‐inject it into the single‐mode fiber in order to seed a cascaded BEFL line in the same direction as the first BEFL line. An efficient BEFL can be obtained by recycling backward a 1550‐nm‐band amplified spontaneous emission as a secondary pump source for the unpumped EDF in the L‐band EDFA section. As a result, the lasing threshold is reduced and slope efficiency is improved. A stable and strong laser comb of up to five lines with 10‐GHz spacing has been obtained with a Brillouin pump of 4.8 mW and a 980‐nm pump of 92 mW. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 506–508, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10650
Mycobacterium bovisBCG Response Regulator Essential for Hypoxic Dormancy
Authors: Boon Calvin , Dick Thomas 
Published: November 2002

ABSTRACTObligately aerobic tubercle bacilli are capable of adapting to survive hypoxia by developing into a nonreplicating or dormant form. Dormant bacilli maintain viability for extended periods. Furthermore, they are resistant to antimycobacterials, and hence, dormancy might play a role in the persistence of tuberculosis infection despite prolonged chemotherapy. Previously, we have grown dormantMycobacterium bovisBCG in an oxygen-limited Wayne culture system and subjected the bacilli to proteome analysis. This work revealed the upregulation of the response regulator Rv3133c and three other polypeptides (α-crystallin and two “conserved hypothetical” proteins) upon entry into dormancy. Here, we replaced the coding sequence of the response regulator with a kanamycin resistance cassette and demonstrated that the loss-of-function mutant died after oxygen starvation-induced termination of growth. Thus, the disruption of this dormancy-induced transcription factor resulted in loss of the ability of BCG to adapt to survival of hypoxia. Two-dimensional gel electrophoresis of protein extracts from the gene-disrupted strain showed that the genetic loss of the response regulator caused loss of the induction of the other three dormancy proteins. Thus, the upregulation of these dormancy proteins requires the response regulator. Based on these two functions, dormancy survival and regulation, we named the Rv3133c genedosRfor dormancy survival regulator. Our results provide conclusive evidence that DosR is a key regulator in the oxygen starvation-induced mycobacterial dormancy response.
Requirement for IscS in Biosynthesis of All Thionucleosides in
Escherichia coli
Authors: Lauhon Charles T. 
Published: November 2002

ABSTRACT

Escherichia coli
tRNA contains four naturally occurring nucleosides modified with sulfur. Cysteine is the intracellular sulfur source for each of these modified bases. We previously found that the
iscS
gene, a member of the
nifS
cysteine desulfurase gene family, is required for 4-thiouridine biosynthesis in
E. coli
. Since IscS does not bind tRNA, its role is the mobilization and distribution of sulfur to enzymes that catalyze the sulfur insertion steps. In addition to
iscS
,
E. coli
contains two other
nifS
homologs,
csdA
and
csdB
, each of which has cysteine desulfurase activity and could potentially donate sulfur for thionucleoside biosynthesis. Double
csdA csdB
and
iscS csdA
mutants were prepared or obtained, and all mutants were analyzed for thionucleoside content. It was found that unfractionated tRNA isolated from the
iscS
mutant strain contained <5% of the level of sulfur found in the parent strain. High-pressure liquid chromatography analysis of tRNA nuclease digests from the mutant strain grown in the presence of [
35
S]cysteine showed that only a small fraction of 2-thiocytidine was present, while the other thionucleosides were absent when cells were isolated during log phase. As expected, digests from the
iscS
mutant strain contained 6-
N
-dimethylallyl adenosine (i
6
A) in place of 6-
N
-dimethylallyl-2-methylthioadenosine and 5-methylaminomethyl uridine (mnm
5
U) instead of 5-methylaminomethyl-2-thiouridine. Prolonged growth of the
iscS
and
iscS csdA
mutant strains revealed a gradual increase in levels of 2-thiocytidine and 6-
N
-dimethylallyl-2-methylthioadenosine with extended incubation (>24 h), while the thiouridines remained absent. This may be due to a residual level of Fe-S cluster biosynthesis in
iscS
deletion strains. An overall scheme for thionucleoside biosynthesis in
E. coli
is discussed.