bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aiding diagnosis of attention‐deficit/hyperactivity disorder and its subtypes: discriminant function analysis of event‐related potential data
Authors: Smith Janette L. , Johnstone Stuart J. , Barry Robert J. 
Published: September 2003

Background: Robust evidence exists that the brain functioning of children and adolescents with attention‐deficit/hyperactivity disorder (AD/HD) differs from that of normal controls. The purpose of this study was to further investigate whether event‐related potential (ERP) measures of brain function could be used to reliably classify normal controls versus children and adolescents with two subtypes of AD/HD.Methods: Behavioural and topographic ERP data from children aged 8–12 years (n = 75) and adolescents aged 13–18 years (n = 75) were entered into stepwise discriminant function analyses separating controls and subjects with AD/HD, and also subjects with AD/HD‐Predominantly Inattentive type (AD/HDin) from those with AD/HD‐Combined type (AD/HDcom).Results: For children aged 8–12 years, controls and children with AD/HD could be separated with an overall classification accuracy of 73.3%, and the AD/HD subtypes were classified with 69.4% overall accuracy. For adolescents aged 13–18 years, 58.7% of the control vs. AD/HD subjects were correctly classified, and 62.7% of subjects in the subtypes. Classification function coefficients for each of these discriminations are presented for the purposes of cross‐validation.Conclusions: In children aged 8–12 years, analysis of ERP data may aid a clinician in diagnosing AD/HD, although the clinical utility of ERP analysis is reduced for adolescents aged 13–18 years. Suggestions are made to combine ERP measures with other measures of brain function in order to improve classification accuracy, and also to predict drug response in children diagnosed with AD/HD.
Corporate Board Composition, Protocols, and Voting Behavior: Experimental Evidence
Authors: Gillette Ann B. , Noe Thomas H. , Rebello Michael J. 
Published: September 2003

AbstractWe examine voting by a board designed to mitigate conflicts of interest between privately informed insiders and owners. Our model demonstrates that, as argued by researchers and the business press, boards with a majority of trustworthy but uninformed “watchdogs” can implement institutionally preferred policies. Our laboratory experiments strongly support this conclusion. Our model also highlights the necessity of penalties on insiders when there is dissension among board members. However, penalties for dissent appeared to have little impact on the experimental outcomes.
Characterization of Hybrid Toluate and Benzoate Dioxygenases
Authors: Ge Yong , Eltis Lindsay D. 
Published: August 2003

ABSTRACT

Toluate dioxygenase of
Pseudomonas putida
mt-2 (TADO
mt2
) and benzoate dioxygenase of
Acinetobacter calcoaceticus
ADP1 (BADO
ADP1
) catalyze the 1,2-dihydroxylation of different ranges of benzoates. The catalytic component of these enzymes is an oxygenase consisting of two subunits. To investigate the structural determinants of substrate specificity in these ring-hydroxylating dioxygenases, hybrid oxygenases consisting of the α subunit of one enzyme and the β subunit of the other were prepared, and their respective specificities were compared to those of the parent enzymes. Reconstituted BADO
ADP1
utilized four of the seven tested benzoates in the following order of apparent specificity: benzoate > 3-methylbenzoate > 3-chlorobenzoate > 2-methylbenzoate. This is a significantly narrower apparent specificity than for TADO
mt2
(3-methylbenzoate > benzoate ∼ 3-chlorobenzoate > 4-methylbenzoate ∼ 4-chlorobenzoate ≫ 2-methylbenzoate ∼ 2-chlorobenzoate [Y. Ge, F. H. Vaillancourt, N. Y. Agar, and L. D. Eltis, J. Bacteriol. 184:4096-4103, 2002]). The apparent substrate specificity of the α
B
β
T
hybrid oxygenase for these benzoates corresponded to that of BADO
ADP1
, the parent from which the α subunit originated. In contrast, the apparent substrate specificity of the α
T
β
B
hybrid oxygenase differed slightly from that of TADO
mt2
(3-chlorobenzoate > 3-methylbenzoate > benzoate ∼ 4-methylbenzoate > 4-chlorobenzoate > 2-methylbenzoate > 2-chlorobenzoate). Moreover, the α
T
β
B
hybrid catalyzed the 1,6-dihydroxylation of 2-methylbenzoate, not the 1,2-dihydroxylation catalyzed by the TADO
mt2
parent. Finally, the turnover of this
ortho
-substituted benzoate was much better coupled to O
2
utilization in the hybrid than in the parent. Overall, these results support the notion that the α subunit harbors the principal determinants of specificity in ring-hydroxylating dioxygenases. However, they also demonstrate that the β subunit contributes significantly to the enzyme's function.
Overproduction of Inactive Variants of the Murein Synthase PBP1B Causes Lysis in
Escherichia coli
Authors: Meisel Ute , Höltje Joachim-Volker , Vollmer Waldemar 
Published: August 2003

ABSTRACT

Penicillin-binding protein 1B (PBP1B) of
Escherichia coli
is a bifunctional murein synthase containing both a transpeptidase domain and a transglycosylase domain. The protein is present in three forms (α, β, and γ) which differ in the length of their N-terminal cytoplasmic region. Expression plasmids allowing the production of native PBP1B or of PBP1B variants with an inactive transpeptidase or transglycosylase domain or both were constructed. The inactive domains contained a single amino acid exchange in an essential active-site residue. Overproduction of the inactive PBP1B variants, but not of the active proteins, caused lysis of wild-type cells. The cells became tolerant to lysis by inactive PBP1B at a pH of 5.0, which is similar to the known tolerance for penicillin-induced lysis under acid pH conditions. Lysis was also reduced in mutant strains lacking several murein hydrolases. In particular, a strain devoid of activity of all known lytic transglycosylases was virtually tolerant, indicating that mainly the lytic transglycosylases are responsible for the observed lysis effect. A possible structural interaction between PBP1B and murein hydrolases in vivo by the formation of a multienzyme complex is discussed.
Jumping the Barrier to β-Lactam Resistance in
Staphylococcus aureus
Authors: Katayama Yuki , Zhang Hong-Zhong , Hong Dong , Chambers Henry F. 
Published: August 2003

ABSTRACT

Although the staphylococcal methicillin resistance determinant,
mecA
, resides on a mobile genetic element, staphylococcus cassette chromosome
mec
(SCC
mec
), its distribution in nature is limited to as few as five clusters of related methicillin-resistant
Staphylococcus aureus
(MRSA) clones. To investigate the potential role of the host chromosome in clonal restriction of the methicillin resistance determinant, we constructed plasmid pYK20, carrying intact
mecA
, and introduced it into several methicillin-susceptible
Staphylococcus aureus
strains, five of which were naive hosts (i.e.,
mecA
not previously resident on the host chromosome) and five of which were experienced hosts (i.e., methicillin-susceptible variants of MRSA strains from which SCC
mec
was excised). We next assessed the effect of the recipient background on the methicillin resistance phenotype by population analysis, by assaying the
mecA
expression of PBP2a by Western blot analysis, and by screening for mutations affecting
mecA
. Each experienced host transformed with pYK20 had a resistance phenotype and expressed PBP2a similar to that of the parent with chromosomal SCC
mec
, but naive hosts transformed with pYK20 selected against its expression, indicative of a host barrier. Either inducible β-lactamase regulatory genes
blaR1
-
blaI
or homologous regulatory genes
mecR1
-
mecI
, which control
mecA
expression, acted as compensatory elements, permitting the maintenance and expression of plasmid-carried
mecA
.
DNA Topoisomerase III from the Hyperthermophilic Archaeon
Sulfolobus solfataricus
with Specific DNA Cleavage Activity
Authors: Dai Penggao , Wang Ying , Ye Risheng , Chen Liang , Huang Li 
Published: August 2003

ABSTRACT

We report the production, purification, and characterization of a type IA DNA topoisomerase, previously designated topoisomerase I, from the hyperthermophilic archaeon
Sulfolobus solfataricus
. The protein was capable of relaxing negatively supercoiled DNA at 75°C in the presence of Mg
2+
. Mutation of the putative active site Tyr318 to Phe318 led to the inactivation of the protein. The
S. solfataricus
enzyme cleaved oligonucleotides in a sequence-specific fashion. The cleavage occurred only in the presence of a divalent cation, preferably Mg
2+
. The cofactor requirement of the enzyme was partially satisfied by Cu
2+
, Co
2+
, Mn
2+
, Ca
2+
, or Ni
2+
. It appears that the enzyme is active with a broader spectrum of metal cofactors in DNA cleavage than in DNA relaxation (Mg
2+
and Ca
2+
). The enzyme-catalyzed oligonucleotide cleavage required at least 7 bases upstream and 2 bases downstream of the cleavage site. Analysis of cleavage by the
S. solfataricus
enzyme on a set of oligonucleotides revealed a consensus cleavage sequence of the enzyme: 5′-G(A/T)CA(T)AG(T)G(A)X↓XX-3′. This sequence bears more resemblance to the preferred cleavage sites of topoisomerases III than to those of topoisomerases I. Based on these data and sequence analysis, we designate the enzyme
S. solfataricus
topoisomerase III.
Epoxyalkane:Coenzyme M Transferase in the Ethene and Vinyl Chloride Biodegradation Pathways of
Mycobacterium
Strain JS60
Authors: Coleman Nicholas V. , Spain Jim C. 
Published: August 2003

ABSTRACT

Mycobacterium
strains that grow on ethene and vinyl chloride (VC) are widely distributed in the environment and are potentially useful for biocatalysis and bioremediation. The catabolic pathway of alkene assimilation in mycobacteria is not well characterized. It is clear that the initial step is a monooxygenase-mediated epoxidation that produces epoxyethane from ethene and chlorooxirane from VC, but the enzymes involved in subsequent transformation of the epoxides have not been identified. We investigated epoxyethane metabolism in
Mycobacterium
strain JS60 and discovered a coenzyme M (CoM)-dependent enzyme activity in extracts from VC- and ethene-grown cells. PCR amplifications using primers targeted at epoxyalkane:CoM transferase (EaCoMT) genes yielded part of the JS60 EaCoMT gene, which was used to clone an 8.4-kb genomic DNA fragment. The complete EaCoMT gene (
etnE
) was recovered, along with genes (
etnABCD
) encoding a four-component monooxygenase and two genes possibly involved in acyl-CoA ester metabolism. Reverse transcription-PCR indicated that the
etnE
and
etnA
genes were cotranscribed and inducible by ethene and VC. Heterologous expression of the
etnE
gene in
Mycobacterium smegmatis
mc
2
155 using the pMV261 vector gave a recombinant strain capable of transforming epoxyethane, epoxypropane, and chlorooxirane. A metabolite identified by mass spectrometry as 2-hydroxyethyl-CoM was produced from epoxyethane. The results indicate that the EaCoMT and monooxygenase enzymes encoded by a single operon (
etnEABCD
) catalyze the initial reactions in both the VC and ethene assimilation pathways. CoM-mediated reactions appear to be more widespread in bacteria than was previously believed.
A Dual Binding Site for Integration Host Factor and the Response Regulator CtrA inside the
Caulobacter crescentus
Replication Origin
Authors: Siam Rania , Brassinga Ann Karen C. , Marczynski Gregory T. 
Published: August 2003

ABSTRACT

The response regulator CtrA controls chromosome replication by binding to five sites, a, b, c, d, and e, inside the
Caulobacter crescentus
replication origin (
Cori
). In this study, we demonstrate that integration host factor (IHF) binds
Cori
over the central CtrA binding site c. Surprisingly, IHF and CtrA share DNA recognition sequences. Rather than promoting cooperative binding, IHF binding hinders CtrA binding to site c and nearby site d. Unlike other CtrA binding sites, DNA mutations in the CtrA c/IHF site uniquely impair autonomous
Cori
plasmid replication. These mutations also alter transcription from distant promoters more than 100 bp away. When the CtrA c/IHF site was deleted from the chromosome, these cells grew slowly and became selectively intolerant to a CtrA phosphor-mimic allele (D51E). Since CtrA protein concentration decreases during the cell cycle as IHF protein concentration increases, we propose a model in which IHF displaces CtrA in order to bend
Cori
and promote efficient chromosome replication.
Autotransporters as Scaffolds for Novel Bacterial Adhesins: Surface Properties ofEscherichia coliCells Displaying Jun/Fos Dimerization Domains
Authors: Veiga Esteban , de Lorenzo Víctor , Fernández Luis Angel 
Published: August 2003

ABSTRACTHybrid proteins containing the β-autotransporter domain of the immunoglobulin A (IgA) protease ofNeisseria gonorrhoea(IgAβ) and the partner leucine zippers of the eukaryotic transcriptional factors Fos and Jun were expressed inEscherichia coli.Such fusion proteins targeted the leucine zipper modules to the cell surface. Cells displaying the Junβ sequence flocculated shortly after induction of the hybrid protein.E. colicells expressing separately Fosβ and Junβ chimeras formed stable bacterial consortia. These associations were physically held by tight intercell ties caused by the protein-protein interactions of matching dimerization domains. The role of autotransporters in the emergence of new adhesins is discussed.
Complete Genome Sequence of the Oral Pathogenic Bacterium
Porphyromonas gingivalis
Strain W83
Authors: Nelson Karen E. , Fleischmann Robert D. , DeBoy Robert T. , Paulsen Ian T. , Fouts Derrick E. , Eisen Jonathan A. , Daugherty Sean C. , Dodson Robert J. , Durkin A. Scott , Gwinn Michelle , Haft Daniel H. , Kolonay James F. , Nelson William C. , Mason Tanya , Tallon Luke , Gray Jessica , Granger David , Tettelin Hervé , Dong Hong , Galvin Jamie L. , Duncan Margaret J. , Dewhirst Floyd E. , Fraser Claire M. 
Published: August 2003

ABSTRACT

The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium
Porphyromonas gingivalis
strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the
Cytophaga-Flavobacteria-Bacteroides
(CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of
P. gingivalis
are those of
Bacteroides thetaiotaomicron
and
B. fragilis
. Outside of the CFB phyla the most similar genome to
P. gingivalis
is that of
Chlorobium tepidum
, supporting the previous phylogenetic studies that indicated that the
Chlorobia
and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that
P. gingivalis
can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.
Disparate Oxygen Responsiveness of Two Regulatory Cascades That Control Expression of Symbiotic Genes in
Bradyrhizobium japonicum
Authors: Sciotti Michel-Angelo , Chanfon Astrid , Hennecke Hauke , Fischer Hans-Martin 
Published: August 2003

ABSTRACT

Two oxygen-responsive regulatory systems controlling numerous symbiotic genes in
Bradyrhizobium japonicum
were assayed in free-living cultures for their capacity to activate target genes under different oxygen conditions. NifA- and FixLJ-controlled target genes showed disparate relative expression patterns. Induction of NifA-dependent genes was observed only at oxygen concentrations below 2% in the gas phase, whereas that of FixLJ-controlled targets progressively increased when the oxygen concentration was lowered from 21 to 5, 2, or 0.5%. We propose that this reflects a response to a gradient of increasing oxygen deprivation as bacteria invade their host during root nodule development.
The Vpu Protein of Human Immunodeficiency Virus Type 1 Plays a Protective Role against Virus-Induced Apoptosis in Primary CD4+T Lymphocytes
Authors: Komoto Satoshi , Tsuji Shoutaro , Ibrahim Madiha S. , Li Yong-Gang , Warachit Jiranan , Taniguchi Koki , Ikuta Kazuyoshi 
Published: September 2003

ABSTRACTPrevious data revealed that primary cultures of peripheral blood mononuclear cells (PBMCs) were killed by apoptosis at higher rates after infection with two CRF01_AE primary isolates of human immunodeficiency virus type 1 (HIV-1) than after infection with five other CRF01_AE primary isolates, five subtype B primary isolates, and two subtype B laboratory strains. Here, we show evidence that mutations at thevpugene which were exclusively identified only in the two CRF01_AE isolates mentioned above are involved in their abilities to induce massive apoptosis in primary CD4+T lymphocytes. The rates of virus production by these two isolates in the culture media of infected PBMCs were lower (the same as those of the other CRF01_AE isolates) than those of the subtype B isolates. To confirm the correlation between the higher apoptosis-inducing abilities and the mutations at thevpugene, infectious molecular clone pNL4-3-basedvpumutants were constructed and examined for their apoptosis induction levels. The apoptosis induction levels after introduction of thevpumutations were greatly increased in primary CD4+T lymphocytes. In contrast, the apoptosis induction abilities of thesevpumutants were lower in human T-cell line MT-4. Thus, the Vpu protein of HIV-1 could play a protective role against virus-induced apoptosis in primary CD4+T lymphocytes.
Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo
Authors: Cornillez-Ty Cromwell T. , Lazinski David W. 
Published: September 2003

ABSTRACT
Hepatitis delta virus expresses two essential proteins, the small and large delta antigens, and both are required for viral propagation. Proper function of each protein depends on the presence of a common amino-terminal multimerization domain. A crystal structure, solved using a peptide fragment that contained residues 12 to 60, depicts the formation of an octameric ring composed of antiparallel coiled-coil dimers. Because this crystal structure was solved for only a fragment of the delta antigens, it is unknown whether octamers actually form in vivo at physiological protein concentrations and in the context of either intact delta antigen. To test the relevance of the octameric structure, we developed a new method to probe coiled-coil structures in vivo. We generated a panel of mutants containing cysteine substitutions at strategic locations within the predicted monomer-monomer interface and the dimer-dimer interface. Since the small delta antigen contains no cysteine residues, treatment of cell extracts with a mild oxidizing reagent was expected to induce disulfide bond formation only when the appropriate pairs of cysteine substitution mutants were coexpressed. We indeed found that, in vivo, both the small and large delta antigens assembled as antiparallel coiled-coil dimers. Likewise, we found that both proteins could assume an octameric quaternary structure in vivo. Finally, during the course of these experiments, we found that unprenylated large delta antigen molecules could be disulfide cross-linked via the sole cysteine residue located within the carboxy terminus. Therefore, in vivo, the C terminus likely provides an additional site of protein-protein interaction for the large delta antigen.
Organization and Expression Strategy of the Ambisense Genome of Densonucleosis Virus of
Galleria mellonella
Authors: Tijssen P. , Li Y. , El-Far M. , Szelei J. , Letarte M. , Zádori Z. 
Published: September 2003

ABSTRACT

The expression strategy of parvoviruses of the
Densovirus
genus has as yet not been reported. Clones were obtained from the densonucleosis virus of
Galleria mellonella
(
Gm
DNV) that yielded infectious virus upon transfection into LD652 cells. Its genome was found to be the longest (6,039 nucleotides [nt]), with the largest inverted terminal repeats (ITRs) (550 nt) among all parvoviruses. The distal 136 nt could be folded into hairpins with flop or flip sequence orientations. In contrast to vertebrate parvoviruses, the gene cassettes for the nonstructural (NS) and structural (VP) proteins were found on the 5′ halves of the opposite strands. The transcripts for both cassettes started 23 nt downstream of the ITRs. The TATA boxes, as well as all upstream promoter elements, were localized in the ITRs and, therefore, identical for the NS and VP transcripts. These transcripts overlapped for 60 nt at the 3′ ends (antisense RNAs) at 50 m.u. The NS cassette consisted of three genes of which NS2 was contained completely within NS1 but from a different reading frame. Most of the NS transcripts were spliced to remove the upstream NS3, allowing leaky scanning translation of NS1 and NS2, similar to the genes of RNA-6 of influenza B virus. NS3 could be translated from the unspliced transcript. The VP transcript was not spliced and generated four VPs by a leaky scanning mechanism. The 5′-untranslated region of the VP transcript was only 5 nt long. Despite the transcription and translation strategies being radically different from those of vertebrate parvoviruses, the capsid was found to have phospholipase A
2
activity, a feature thus far unique for parvoviruses.
Recombination in Circulating Enteroviruses
Authors: Lukashev Alexander N. , Lashkevich Vasilii A. , Ivanova Olga E. , Koroleva Galina A. , Hinkkanen Ari E. , Ilonen Jorma 
Published: September 2003

ABSTRACT
Recombination is a well-known phenomenon for enteroviruses. However, the actual extent of recombination in circulating nonpoliovirus enteroviruses is not known. We have analyzed the phylogenetic relationships in four genome regions, VP1, 2A, 3D, and the 5′ nontranslated region (NTR), of 40 enterovirus B strains (coxsackie B viruses and echoviruses) representing 11 serotypes and isolated in 1981 to 2002 in the former Soviet Union states. In the VP1 region, strains of the same serotype expectedly grouped with their prototype strain. However, as early as the 2A region, phylogenetic grouping differed significantly from that in the VP1 region and indicated recombination within the 2A region. Moreover, in the 5′ NTR and 3D region, only 1 strain of 40 grouped with its prototype strain. Instead, we observed a major group in both the 5′ NTR and the 3D region that united most (in the 5′ NTR) or all (in the 3D region) of the strains studied, regardless of the serotype. Subdivision within that major group in the 3D region correlated with the time of virus isolation but not with the serotype. Therefore, we conclude that a majority, if not all, circulating enterovirus B strains are recombinants relative to the prototype strains, isolated mostly in the 1950s. Moreover, the ubiquitous recombination has allowed different regions of the enterovirus genome to evolve independently. Thus, a novel model of enterovirus genetics is proposed: the enterovirus genome is a stable symbiosis of genes, and enterovirus species consist of a finite set of capsid genes responsible for different serotypes and a continuum of nonstructural protein genes that seem to evolve in a relatively independent manner.