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PubMed1997

A highly conserved DNA replication module from Streptococcus thermophilus phages is similar in sequence and topology to a module from Lactococcus lactis phages.

A highly conserved DNA region extending over 5 kb was observed in Streptococcus thermophilus bacteriophages. Comparative sequencing of one temperate and 26 virulent phages demonstrated in the most extreme case an 18% aa difference for a predicted protein, while the majority of the phages showed fewer, if any aa changes. The relative degree of aa conservation was not homogeneous over the DNA segment investigated. Sequence analysis of the conserved segment revealed genes possibly involved in DNA transactions. Three predicted proteins (orf 233, 443, and 382 gene product (gp)) showed nucleoside triphosphate binding motifs. Orf 443 gp showed in addition a DEAH box motif, characteristically found in a subgroup of helicases, and a variant zinc finger motif known from a phage T7 helicase/primase. Tree analysis classified orf 443 gp as a distant member of the helicase superfamily. Orf 382 gp showed similarity to putative plasmid DNA primases. Downstream of orf 382 a noncoding repeat region was identified that showed similarity to a putative minus origin from a cryptic S. thermophilus plasmid. Four predicted proteins showed not only high degrees of aa identity (34 to 63%) with proteins from Lactococcus lactis phages, but their genes showed a similar topological organization. We interpret this as evidence for a horizontal gene transfer event between phages of the two bacterial genera in the distant past.

Amino Acid Sequence↗
PubMed1995

Isolation and in vitro phosphorylation of sensory transduction components controlling anaerobic induction of light harvesting and reaction center gene expression in Rhodobacter capsulatus.

Anaerobic induction of light harvesting and reaction center gene expression involves two transacting factors termed RegA and RegB. Sequence and mutational analysis has indicated that RegA and RegB constitute cognate components of a prokaryotic sensory transduction cascade with RegB comprising a membrane-spanning sensor kinase and RegA a cytosolic response regulator. In this study we have purified RegA, as well as a truncated portion of RegB (RegB') and undertaken an in vitro analysis of autophosphorylation and phosphotransfer activities. Incubation of RegB' with [gamma-32P]ATP and MgCl2 resulted in phosphorylation of RegB' (RegB' approximately P) over a 20-min incubation period. Incubation of RegB' approximately P with RegA resulted in rapid transfer of the phosphate from RegB' to RegA. In analogy to other characterized prokaryotic sensory transduction components, mutational and chemical stability studies also indicate that RegB' is autophosphorylated at a conserved histidine and that RegA accepts the phosphate from RegB at a conserved aspartate.

Bacterial Proteins↗
PubMed2001

Tobacco-smoke-inducible human haem oxygenase-1 gene expression: role of distinct transcription factors and reactive oxygen intermediates.

Exposure of eukaryotic cells to a variety of reactive-oxygen-intermediate (ROI)-mediated sources of cellular injury, including heavy metals and UV radiation, induces the expression of heat-shock (HS) and stress-related genes among which is a 32-34 kDa protein identified as inducible haem oxygenase-1 (HO-1). We previously showed that tobacco smoke (TS), a potent source of oxidants leading to oxidative stress, induces both HS proteins (HSPs) and HO-1 in normal human monocytes. Here we investigated the induction mechanisms of human HO-1 gene expression by TS in the human premonocytic line U937. Northern blotting and flow cytometry revealed a dose- and time-dependent induction of HO-1 mRNA and protein by TS. In order to clarify the role of transacting factors in this induction, electrophoretic mobility-shift analysis was performed with nuclear extracts from control, TS-, cadmium (Cd)- or H(2)O(2)-exposed cells, incubated with consensus elements and binding sites of the promoter region of HO-1[heat-shock factor (HSF), nuclear factor kappaB (NF-kappaB) and activator protein-1 (AP-1)] and the cadmium-responsive element (CdRE) isolated by Takeda, Ishizawa, Sato, Yoshida and Shibahara [(1994) J. Biol. Chem. 269, 22858-22867]. We report an inhibition of NF-kappaB activation by TS, no effect on AP-1 and a strong activation of CdRE-binding activity, whereas cadmium chelation from TS only partially prevented HO-1 induction. H(2)O(2) also activated the CdRE-binding activity, and pretreatment with N-acetyl-L-cysteine, which replenishes the intracellular levels of GSH, suppressed, in TS-treated cells, both the CdRE-binding activity and the increased HO-1 expression.

Base Sequence↗
PubMed2005

Including non-point sfources in a water quality trading permit program.

There has been overwhelming interest in addressing water quality issues through the use of economic instruments. Much of this attention has focused on the cost efficiencies offered by Transferable Discharge Permit (TDP) systems. Unfortunately, the attempts to start up permit markets which are able to exploit abatement cost differences between sources have not met with the success expected. Two of the reasons for the lack of success that have been taken up in analysis of these programs have been the problem of transaction costs and in the case of non-point sources (NPS), undefined property rights. The composite market design is a proposal for a TDP system which specifically includes agricultural non-point source (NPS) dischargers and addresses both property rights and transaction cost problems. The composite market consists of three interrelated markets each serving a particular function. When the composite market is mature, the total number of permits issued represents the cap on discharges allowed in the catchment. The structure of the composite market allows this system to be phased in over time with existing institutions and limited demands on financing.

Commerce↗
PubMed1997

Genetic analysis of internal ribosomal entry site on hepatitis C virus RNA: implication for involvement of the highly ordered structure and cell type-specific transacting factors.

Hepatitis C virus (HCV) carries an internal ribosomal entry site (IRES) within the 5' portion of the RNA. To identify structures that influence efficiency of the translation initiation, relative activities of modified IRESs were examined by using engineered bicistronic mRNAs, between the two cistrons of which various mutant IRESs were inserted. An IRES derived from genotype 2b is at least two times more efficient than one from genotype 1b in cultured cells. Activity ratios of genotype 2b IRES to 1b IRES differ in magnification among cultured cells, suggesting the difference in assortment of IRES-related host factors among individual cell types. Recombinant IRESs between the genotypes show similar or higher activities compared with 2b IRES in cell-free systems and show intermediate activities in cultured cells. Patterns of relative activities of those IRESs indicate that the IRES activity is not regulated by defined structure(s), although a cluster of different nucleotides is observed in the genome region of nucleotides 176-224 between the two alleles. The results suggest that a highly ordered structure formed by the entire 5' portion of the RNA is important for the IRES activity. The 5' border of HCV IRES was examined by using a series of deletion RNAs in various systems. The results strongly suggest that the border resides between nucleotide positions 28 and 45. Patterns of relative activities of the deletion IRESs differ in translation systems or cell types. These results imply that interactions of HCV RNA with the related transacting factor(s) may differ in the translation systems or cell types.

Base Sequence↗
PubMed2004

[Comprehensive evaluation of cultivated black soil fertility].

Black soil is one of the main soil types in northeastern China, and is a valuable soil resource of this country. Based on the analysis of the physical and chemical properties of soil samples collected from the north-south transaction of black soil, the index system of black soil fertility was established, the fertility level was evaluated and classified by Fuzzy and Factor Analysis, and the fertility map of black soil zone was drawn with GIS software ArcInfo. It was found that the humus layer in black soil region was thick in north and thin in south, which was due to the climatic condition and soil-forming process. The soil fertility level was high in east and low in west. From north to south, it was decreased in the order of central part > northern part > south part. In most part of this region, soil fertility level was medium, and the area accounted for 73.6% of the black soil area.

China↗
PubMed1993

Effects of training in time-limited dynamic psychotherapy: mediators of therapists' responses to training.

Sixteen therapists were enrolled in a year-long manualized training program as part of the Vanderbilt II study of time-limited dynamic psychotherapy (TLDP). The training program successfully changed therapists' interventions in line with prescriptions of the TLDP manual, but some unanticipated changes ran counter to the intent of the training, including increased negative interpersonal transactions as indicated by process measures such as the Structural Analysis of Social Behavior (SASB). We examined therapist variables, patient variables, and training variables that appeared to mediate therapist responses to the training program. Results indicate that patient difficulty may mediate certain aspects of therapists' responses to training. Therapists with self-reported hostile and controlling introjects showed the greatest technical adherence, which was intriguing because prior research has linked hostile therapist introject to greater frequency of counter-therapeutic interpersonal process. Of special interest were differences in effects of training associated with individual training faculty. This finding, if generalizable, has important implications for manualized therapy research, especially multisite trials.

Adult↗
PubMed1993

A transcription factor with homology to the AP-1 family links RNA transcription and DNA replication in the lytic cycle of Epstein-Barr virus.

oriLyt, the lytic origin of DNA replication of Epstein-Barr virus (EBV), ensures viral DNA amplification during the productive or lytic phase of the virus' life cycle. To understand the contribution of cis- and transacting elements involved in DNA replication of oriLyt, a detailed mutational analysis was undertaken which defined BZLF1, a viral transcriptional activator, as an essential replication factor. The BZLF1 protein belongs to the extended fos/jun family of transcription factors and binds to specific BZLF1 binding motifs within oriLyt, as well as to consensus AP-1 sites. Recombinant, chimeric transcription factors identified the transcriptional activation domain of BZLF1 as being necessary to mediate DNA replication, a function which could not be substituted by any other transcription factor tested, including jun, E2, myc or VP16.

Binding Sites↗
PubMed1994

Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility.

The parA partitioning system of plasmid R1 consists of three different components: the cis-acting centromere-like parC site, and the two trans-acting proteins ParM and ParR. These three components are contained within a region of 1.6 kb. The parC site is located upstream of the two genes, parM and parR, which are expressed as an operon from the parA promoter. The parC site contains an array of ten 11 base-pair direct repeats, organized in two sets of five repeats flanking the parA core promoter sequences. Deletions and point mutations were introduced in the parA locus, resulting in partially stable and unstable plasmids. An analysis of these parA- plasmids showed that ParM and ParR are transacting. The 160 bp minimal parC region contained sufficient in cis information for efficient trans-complementation. Both proteins were required for maximal stabilization of a parC+ mini-R1 plasmid, although ParR alone, donated either in cis or in trans, yielded partial stabilization. Plasmids that overexpressed ParR caused destabilization of a co-resident parA+ plasmid, whereas overexpression of ParM had no such effect. The parC site exerted incompatibility (incA) at high but not at low copy number. Likewise, the entire parA system exerted incompatibility in a copy number-dependent fashion, and stronger than the incompatibility expressed by parC alone.

Base Sequence↗
PubMed2000

Active segregation by the Bacillus subtilis partitioning system in Escherichia coli.

Bacterial genes required for proper partitioning consist of two transacting genes that encode proteins and a cis-acting gene that functions like a centromere. Plasmids actively partitioning by means of these genes migrate from midcell to the cell quarters and are tethered to these sites until the cells divide. Previously the partitioning genes were mainly found on plasmids and phages in Escherichia coli. However, progress in genome sequencing reveals that partitioning genes are ubiquitous in many bacterial plasmids and chromosomes. Each homologue of the two transacting genes belongs to a family, ParA or ParB. Moreover, phylogenic analysis of members of the ParA and ParB families indicates that each member falls into a chromosomal group or an extrachromosomal group. It is known that the parAB genes in the chromosomal group are located on relatively conserved chromosomal regions in several bacterial species. This suggests that the parAB genes were transferred from a chromosome to plasmids and phages, so the genes have diverged among bacterial species. To support this possibility, we show that the Bacillus subtilis Soj and Spo0J members of the ParAB families are responsible for the specific localization of plasmids at cell quarters in E. coli and can function as partition proteins. Host factors to tether actively partitioning plasmids at subcellular sites may be conserved in Gram-negative and Gram-positive bacteria so that phages and plasmids with the ParAB partitioning system can be stably inherited in host cells across bacterial species.

Adenosine Triphosphatases↗
PubMed1990

The mobilization and origin of transfer regions of a Thiobacillus ferrooxidans plasmid: relatedness to plasmids RSF1010 and pSC101.

The components for the mobilization function of a plasmid DNA during conjugation include a cis-acting sequence (the origin of transfer, oriT) and a transacting sequence coding for mobilization (Mob) proteins. By genetic and deletion analysis, we have located the mobilization region of pTF1, a cryptic plasmid previously isolated from a Thiobacillus ferrooxidans strain. Within a 2797 bse-pair sequenced region, several open reading frames (ORFs) were predicted; two of the ORFs are divergently transcribed and they encode proteins of calculated molecular masses, 42.6kD (ORF2) and 11.4kD (ORF6). Surprisingly, these protein sequences are substantially similar to two of the previously characterized mobilization proteins of the Escherichia coli IncQ plasmid, RSF1010. Moreover, the pTF1 ORF2 (now designated MobL) sequence is also found to be similar to a presumed mobilization protein of plasmid pSC101. Regions of sequence identity of plasmids pTF1, RSF1010 and pSC101 include their oriT sites. By alkaline agarose gel electrophoresis and DNA sequencing, we have established the location of the relaxation complex nick site within the oriT of pTF1. An identical nick site, which is adjacent to a characteristic 10 base-pair inverted repeat sequence, is also found for plasmid RSF1010. A recombinant plasmid containing a 42 base-pair synthetic piece of DNA encompassing the pTF1 inverted repeat and nick sequence was shown to be oriT-active.

Amino Acid Sequence↗
PubMed1999

In vivo analysis of retroviral integrase structure and function.

There are two retroviral integration loci. One encodes the transacting IN protein, which is cleaved from the carboxyl terminus of the Gag-Pol polyprotein precursor during virus assembly. The second locus is the cis-acting attachment (att) site, comprising the terminal sequences at the U3 and U5 ends of linear viral cDNA. Integrase and att site mutant viruses can be blocked at different steps of the viral replication cycle. Class I IN mutants are blocked specifically at the integration step. Class II IN mutants, on the other hand, display pleiotropic defects, most notably in virion morphogenesis and/or reverse transcription. Mutations in the U5 end att site can also disrupt reverse transcription in addition to integration. It is prudent to use caution when interpreting results of in vivo mutagenesis experiments that target retroviral IN and the att site.

Animals↗
PubMed2006

Network analysis of online bidding activity.

With the advent of digital media, people are increasingly resorting to online channels for commercial transactions. The online auction is a prototypical example. In such online transactions, the pattern of bidding activity is more complex than traditional offline transactions; this is because the number of bidders participating in a given transaction is not bounded and the bidders can also easily respond to the bidding instantaneously. By using the recently developed network theory, we study the interaction patterns between bidders (items) who (that) are connected when they bid for the same item (if the item is bid by the same bidder). The resulting network is analyzed by using the hierarchical clustering algorithm, which is used for clustering analysis for expression data from DNA microarrays. A dendrogram is constructed for the item subcategories; this dendrogram is compared to a traditional classification scheme. The implication of the difference between the two is discussed.

Journal Article↗
PubMed2003

Moving research on resilience into the 21st century: theoretical and methodological considerations in examining the biological contributors to resilience.

Empirical investigations of resilience over the past 30 years have examined a wide range of psychosocial correlates of, and contributors to, this phenomenon. Thus far, theoretical treatments of resilience have focused almost exclusively on psychosocial levels of analysis to derive explanatory models. However, there have been no formal discussions of either theory or research that have examined the biological contributors to, or correlates of, competent functioning despite the experience of adversity. This paper seeks to fill this gap and sets forth a preliminary theoretical framework and outline of empirical strategies for studying the biological underpinnings of resilience. The initial sections of the paper discuss the particular suitability of a transactional organizational theoretical perspective as a conceptual foundation for including a biological level of analysis within the extant theoretical framework of resilience. Subsequently, other important theoretical considerations for the inclusion of a biological perspective on resilience are discussed, including the avoidance of an approach that would reduce resilience to merely a biological process, the application of the constructs of multifinality and equifinality to a biological perspective on resilience, as well as a general discussion of the potential for utilization of brain imaging and other technologies in the study of resilience. The possible relation between the mechanisms of neural plasticity and resilience are examined in some detail, with specific suggestions concerning research questions needed to examine this association. Sections of the paper discuss the likely relation of several areas of brain and biological functioning with resilience, including emotion, cognition, neuroendocrine and immune functioning, and genetics. The paper concludes with a discussion of the implications of a biological perspective on resilience for preventive interventions.

Affect↗
PubMed2003

Resveratrol and quercetin down-regulate tissue factor expression by human stimulated vascular cells.

BACKGROUND: Epidemiological studies have shown that consumption of wine reduces the risk of coronary heart disease. Resveratrol and quercetin, two polyphenolic compounds found in grapes and red wine, have been shown to contribute to this protection by exerting several biological properties which could be associated with cardioprotection. Tissue factor (TF), the cellular receptor that initiates blood coagulation, plays a primary role both in hemostasis following tissue injury and in the pathogenesis of atherosclerosis which predisposes to thrombosis. OBJECTIVES: We investigated the role of resveratrol and quercetin on TF expression by endothelial and mononuclear cells (MN). METHODS: Confluent human umbilical vein endothelial cells and MN collected from healthy donors were stimulated with bacterial lipopolysaccharide, interleukin-1beta or tumor necrosis factor-alpha after incubation with increasing concentrations of resveratrol or quercetin. RESULTS: In both cell types, TF activity induced by any agonist was significantly reduced by resveratrol or quercetin in a dose-dependent fashion. Northern blot analysis indicated that resveratrol and quercetin strongly reduce TF mRNA in both cell types. The inhibition of TF mRNA originated from a reduction in nuclear binding activity of the transacting factor c-Rel/p65, which was induced by the agonists and measured by electromobility shift assay. Western blot analysis revealed that the diminished c-Rel/p65 activity was dependent upon inhibition of degradation of the c-Rel/p65 inhibitory protein IkappaBalpha. CONCLUSIONS: These results provide a molecular basis which could help explain the protective activity of red wine against cardiovascular disease.

Active Transport, Cell Nucleus↗
PubMed2003

E-business in health care: does it contribute to strengthen consumer interest?

One of the goals of the reforms in the European health-care systems over the last two decades has been to make the health-care system more demand-oriented. There is not much known about the possible impact of E-business like approaches on this goal. This paper describes the concept of E-business. Two cases are introduced to illustrate the use of a simple E-business approach in a health-care setting. On the basis of these case studies, we aspect a reduction of the information disadvantages of patients. In our analysis, we also apply new institutional economy concepts, namely agency theory and transaction costs economics to focus on the position of the patient. Concluded is that it is more probable that preferences of demanders are answered by the suppliers of health care.

Budgets↗
PubMed1990

Dysfunction in the single-parent and only-child family.

As the average size of the family decreases, controversy over the child at risk in relation to family structure has intensified. There is a great deal of literature on single-parent families, but little delineation of specific subgroups. In this pilot study, twelve adolescent inpatients who were an "only child" in single-parent families were compared to a control group of adolescent patients matched for sex, family income, and diagnosis. In some "minimal families" (single parent/only child), the interpersonal transactions were examined as the crucial parameter in formation of dysfunction. Statistical analysis of the data supported the hypothesis that in this clinical sample, the single-parent/only-child families and their adolescents would display a greater degree of disturbance than the control group. Some theoretical and clinical issues related to this group are discussed.

Adaptation, Psychological↗