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Ligand binding sites of the ouabain-complexed (Na+ + K+)-ATPase.

To clarify the mechanism of inhibition of (Na+ + K+)-ATPase by cardiac glycosides, we tried to see if ouabain binding alters the properties of the binding sites for Na+, K+, and ATP. Ouabain was bound in the presence of either Na+ + MgATP or MgPi. Ligand-induced changes in the rate of release of ouabain from the two resulting complexes were used as signals to determine the affinities, the numbers, and the interactions of the ligand binding sites. Because the two complexes showed differences in the properties of their ligand binding sites, and since neither complex could be converted to the other, it is concluded that either the enzyme has two dissimilar but mutually exclusive ouabain sites or that it can be frozen in two distinct conformations by ouabain. The following ligand sites were identified on the two complexes: 1) two coexisting ATP sites (K0.5 values, 0.1 and 2 mM) representing altered states of the catalytic and the regulatory sites of the native enzyme; 2) mutually exclusive Na+ and K+ sites whose affinities (K0.5 values, 1.3 mM Na+ and 0.1 mM K+) suggested their identities with the high affinity uptake sites of the native enzyme; and 3) coexisting low affinity Na+ and K+ sites (K0.5 values, 0.2-0.6 M) representing either the discharge sites, or the regulatory sites, or the access channels of the native enzyme. The data suggest that the inability of the ouabain-complexed enzyme to participate in the normal reaction cycle is not because of its lack of ligand binding sites but most likely due to ouabain-induced disruptions of interprotomer site-site interactions.

Animals↗

Coexpression of glutamine synthetase and carbamoylphosphate synthase I genes in pancreatic hepatocytes of rat.

In the mammalian liver the distribution of ammonia-detoxifying enzymes, glutamine synthetase (GS) and carbamoylphosphate synthase I (ammonia) (CPS-I), is mutually exclusive in that these enzymes are expressed in two distinct populations of hepatocytes that are zonally demarcated in the liver acinus. In the present study we examined the distribution of GS and CPS-I in pancreatic hepatocytes to ascertain if the expression of these two genes in these hepatocytes is also mutually exclusive. Multiple foci of hepatocytes showing no clear acinar organization develop in the adult rat pancreas as a result of a change in the differentiation commitment after dietary copper deficiency. Unlike liver, GS and CPS-I are detected by immunofluorescence in all pancreatic hepatocytes. In situ hybridization revealed that all pancreatic hepatocytes contain GS and CPS-I mRNAs. The sizes of these two mRNAs in pancreas with hepatocytes are similar to those of the liver. The concomitant expression of GS and CPS-I genes in pancreatic hepatocytes may be attributed, in part, to the absence of portal blood supply to the pancreas vis-à-vis the lack of hormonal/metabolic gradients as well as to possible matrix homogeneity in the pancreas.

Animals↗

Frequent monoallelic deletion of PTEN and its reciprocal associatioin with PIK3CA amplification in gastric carcinoma.

Mutational alterations of PTEN and PIK3CA, which negatively and positively regulate PI3-kinase activity, respectively, have been observed in many types of human cancer. To explore the implication of PTEN and PIK3CA mutations in gastric tumorigenesis, we characterized the expression and mutation status of the genes in 126 gastric tissues and 15 cell lines. Expression of PTEN transcript was abnormally low in 5 of 15 (33%) cell lines and 20 of 55 (36%) primary carcinomas, whereas 0 of 71 noncancerous tissues including 16 benign tumors showed altered expression. Allelotyping analysis using an intragenic polymorphism (IVS4+109) revealed that 14 of 30 (47%) informative cases carried LOH of the gene, which is closely linked to low expression. The LOH rate was significantly higher in advanced tumors [12 of 19 (63%)] compared to early-stage tumors [2 of 11 (18%)] and more frequent in poorly differentiated tumors [9 of 13 (69%)] than well- or moderately differentiated tumors [5 of 17 (29%)]. Interestingly, however, none of the LOH tumors carried mutational disruption of the remaining allele, suggesting haploinsufficiency of PTEN in gastric tumorigenesis. Methylation studies revealed that PTEN pseudogene, but not PTEN, is methylated in cell lines and primary tumors, indicating that PTEN is not a target of epigenetic silencing in gastric cancers and that the pseudogene should be considered more carefully in methylation analysis of the PTEN promoter. Genomic amplification of PIK3CA was found in 9 of 15 (60%) cell lines and 20 of 55 (36.4%) primary tumors but in no noncancerous tissues. Furthermore, PIK3CA amplification was predominantly detected in tumors with no PTEN alterations, suggesting that mutations of PTEN and PIK3CA are mutually exclusive events in gastric tumorigenesis. Amplification of PIK3CA was strongly associated with increased expression of PIK3CA transcript and elevated levels of phospho-AKT. Collectively, our data reveal that 13 of 15 (87%) gastric cell lines and 31 of 55 (56%) primary carcinomas harbored either amplification of PIK3CA or abnormal reduction of PTEN. Mutually exclusive alterations of PTEN and PIK3CA also suggest that mutations of either gene could activate the PI3-kinase/AKT signaling pathway, which is directly linked to the malignant progression of gastric tumor cells.

Adenocarcinoma↗

Wavelet analysis can sensitively describe dynamics of ethanol evoked local field potentials of the slug (Limax marginatus) brain.

Odorants evoke characteristic, but complex, local field potentials (LFPs) in the molluscan brain. Wavelet tools in combination with Fourier analysis can detect and characterize hitherto unknown discrete, slow potentials underlying the conspicuous oscillations. Ethanol was one of the odorants that we have extensively studied (J. Neurosci. Methods, 119 (2002) 89). To detect new features and to elucidate their functions, we tested the wavelet tools on the ethanol-evoked LFP responses of the slug (Limax) procerebrum. Recordings were made in vitro from the neuropile and the cell layer. The present study led to the following findings: (i) Mutual exclusion. Energy concentrated mainly in two ranges, (a) 0.1-0.4 Hz and (b) 1.56-12.5 Hz, and the sum of energy remained constant throughout experiments regardless of the condition. A redistribution of relative energy within this sum seemed to occur in the course of main, possible interactions between the two components excluding each other ('mutual exclusion'). (ii) Transient signal ordering and disordering. Ethanol stimulation alternatingly evoked periods of strongly time evolving oscillation dominated by the energy of 1.56-12.5 Hz (increase of entropy=disordered or complexly ordered state) and those of near-silence were predominated by the energy of 0.1-0.4 Hz (decrease of entropy=ordered state). (iii) About 0.1 Hz slow wave oscillation. It was robust. The dominant energy oscillation and the resulting large entropy fluctuation were negatively correlated to each other, and revealed strong frequency-tuning or synchronization at this frequency. Our findings suggest that discrete slow waves play functionally important roles in the invertebrate brain, as widely known in vertebrate EEG. Wavelet tools allow an easy interpretation of several minutes of frequency variations in a single display and give precise information on stimulus-evoked complex change of the neural system describing the new state 'more ordered' or 'non-ordered or more complexly ordered'.

Animals↗

Collagenase-3 (MMP-13) and integral membrane protein 2a (Itm2a) are marker genes of chondrogenic/osteoblastic cells in bone formation: sequential temporal, and spatial expression of Itm2a, alkaline phosphatase, MMP-13, and osteocalcin in the mouse.

Endochondral bone formation requires the action of cells of the chondrocytic and osteoblastic lineage, which undergo continuous differentiation during this process. To identify subpopulations of resting, proliferating, and hypertrophic chondrocytes and osteoblasts involved in bone formation, we have identified here two novel marker genes present in endochondral and intramembranous ossification. Using Northern blot analysis and in situ hybridization on parallel sections of murine embryos and bones of newborn mice we compared the expression pattern of the recently cloned Itm2a and MMP-13 (collagenase-3) genes with that of established marker genes for bone formation, such as alkaline phosphatase (ALP), osteocalcin (OC), and collagen type X, during endochondral and intramembranous ossification. During embryonic development expression of Itm2a and ALP was detectable at midgestation (11.5 days postcoitum [dpc]) and increased up to 16.5 dpc. MMP-13 and OC expression started at 14.5 dpc and 16.5 dpc, respectively. This temporal expression was reflected in the spatial distribution of these markers in the growth plate of long bones. In areas undergoing endochondral ossification Itm2a expression was found in chondrocytes of the resting and the proliferating zones. Expression of ALP and MMP-13 are mutually exclusive: ALP transcripts were found only in collagen type X positive hypertrophic chondrocytes of the upper zone. MMP-13 expression was restricted to chondrocytes of the lower zone of hypertrophic cartilage also expressing collagen type X. In osteoblasts involved in endochondral and intramembranous ossification Itm2a was not present. ALP, MMP-13, and OC were mutually exclusively expressed in these cells suggesting a differentiation-dependent sequential expression of ALP, MMP-13, and OC. The identification of the continuum of sequential expression of Itm2a, ALP, MMP-13, and OC will now allow us to establish a series of marker genes that are highly suitable to characterize bone cells during chondrocytic and osteoblastic differentiation in vivo.

Alkaline Phosphatase↗

Interaction of six global transcription regulators in expression of manganese superoxide dismutase in Escherichia coli K-12.

Transcription of the sodA gene of Escherichia coli, which encodes manganese superoxide dismutase, is governed by six global regulators: the product of the soxRS locus (superoxide response) and mutated alleles of the soxQ locus (such as cfxB) act as activators; the products of the fur (ferric uptake regulation), arcA (aerobic regulation control), and fnr (fumarate nitrate reductase) genes and the integration host factor (IHF) negatively regulate sodA. The action of these effectors on the sodA promoter was investigated by using chromosomal sodA-lacZ operon fusions with intact or deleted promoters, different environmental conditions, and strains carrying different combinations of null mutations in the effector genes. The data allow us to assign target regions in the sodA promoter for activation by SoxRS and CfxB and for repression by Fur and ArcA. In aerobiosis, activation of sodA transcription by SoxRS was compatible with CfxB activation or Fur repression, whereas cfxB and fur controls were mutually exclusive. Repression by Fnr appeared, at least in part, to be ArcA dependent. IHF enhanced aerobic Fur repression, and in the absence of Fur, it enhanced anaerobic repression by ArcA. The DNA targets for Fur (encompassing the -35 region) and ArcA (from and downstream of the -35 region) appear to overlap, suggesting that Fur and ArcA repressions are mutually exclusive. Fur (in response to the iron pool) or ArcA, acting with Fnr and IHF (in response to the redox state of the cells), can block anaerobic sodA-lacZ expression with about equivalent efficiencies. The possible biological significance of this result is discussed.

Bacterial Outer Membrane Proteins↗

Reflection on the history, coordination, and funding trends for U.S. public meat research: information to enhance resource allocation.

A study was conducted to analyze resource allocation for public meat research in the United States and characterize the portfolio of meat research investments. Trends in the amount of public resources provided for meat research (beef, pork, lamb, and poultry) were analyzed for fiscal years 1980, 1985, 1990, 1995, and 1997. An in-depth analysis was conducted for data from fiscal year 1998 to characterize the profile of the research portfolio. Funding levels and scientist-year equivalents were aggregated to represent the measures of resource allocation for three mutually exclusive research categories: 1) meat quality, 2) food safety, and 3) product development and processing. Data for the 1998 profile analysis were derived from a computer search based on the combination of key words and research classification codes to avoid duplication and cluster research projects. Individual research projects were individually reviewed and a percentage was assigned to four mutually exclusive research categories: 1) meat quality, 2) food safety, 3) product development and processing, and 4) marketing. As meat research evolved over the past century, considerable efforts were expended by researchers and administrators to ensure the coordination of research and program relevance. This is demonstrated by the establishment of numerous multistate research committees. Total funding for meat science increased only modestly when adjusted for inflation during the two decades of this study; however, notable changes occurred in the distribution of resources in the portfolio. Funding for meat quality and product development and processing remained virtually unchanged when adjusted for inflation, whereas funding for food safety increased considerably. The total number of scientists conducting meat research remained virtually unchanged during the period, but the proportion allocated to food safety research increased substantially. The federal portion of total funding decreased from 61.3% to 51.6% between 1980 and 1997, whereas the percentage from both state appropriations and private sources increased. Modifications in research emphasis were influenced by industry problems such as meat quality, public perceptions about food safety, the availability of research funding, scientific advances occurring in molecular biology and genetic manipulation, and the changing meat industry. The information in this paper provides administrators and researchers the opportunity to make better informed decisions about resource allocation for meat research.

Advertising↗

Reliability analysis based on the losses from failures.

The conventional reliability analysis is based on the premise that increasing the reliability of a system will decrease the losses from failures. On the basis of counterexamples, it is demonstrated that this is valid only if all failures are associated with the same losses. In case of failures associated with different losses, a system with larger reliability is not necessarily characterized by smaller losses from failures. Consequently, a theoretical framework and models are proposed for a reliability analysis, linking reliability and the losses from failures. Equations related to the distributions of the potential losses from failure have been derived. It is argued that the classical risk equation only estimates the average value of the potential losses from failure and does not provide insight into the variability associated with the potential losses. Equations have also been derived for determining the potential and the expected losses from failures for nonrepairable and repairable systems with components arranged in series, with arbitrary life distributions. The equations are also valid for systems/components with multiple mutually exclusive failure modes. The expected losses given failure is a linear combination of the expected losses from failure associated with the separate failure modes scaled by the conditional probabilities with which the failure modes initiate failure. On this basis, an efficient method for simplifying complex reliability block diagrams has been developed. Branches of components arranged in series whose failures are mutually exclusive can be reduced to single components with equivalent hazard rate, downtime, and expected costs associated with intervention and repair. A model for estimating the expected losses from early-life failures has also been developed. For a specified time interval, the expected losses from early-life failures are a sum of the products of the expected number of failures in the specified time intervals covering the early-life failures region and the expected losses given failure characterizing the corresponding time intervals. For complex systems whose components are not logically arranged in series, discrete simulation algorithms and software have been created for determining the losses from failures in terms of expected lost production time, cost of intervention, and cost of replacement. Different system topologies are assessed to determine the effect of modifications of the system topology on the expected losses from failures. It is argued that the reliability allocation in a production system should be done to maximize the profit/value associated with the system. Consequently, a method for setting reliability requirements and reliability allocation maximizing the profit by minimizing the total cost has been developed. Reliability allocation that maximizes the profit in case of a system consisting of blocks arranged in series is achieved by determining for each block individually the reliabilities of the components in the block that minimize the sum of the capital, operation costs, and the expected losses from failures. A Monte Carlo simulation based net present value (NPV) cash-flow model has also been proposed, which has significant advantages to cash-flow models based on the expected value of the losses from failures per time interval. Unlike these models, the proposed model has the capability to reveal the variation of the NPV due to different number of failures occurring during a specified time interval (e.g., during one year). The model also permits tracking the impact of the distribution pattern of failure occurrences and the time dependence of the losses from failures.

Journal Article↗

The future of research in understanding and controlling work-related low back disorders.

Our knowledge of low back disorder (LBD) causation has progressed well over the years with in-depth understanding accelerating in the traditional disciplines of biomechanics, psychology, psychophysics, psychosocial, physiology, genetics, organizational psychology and rehabilitation. However, each of these disciplines has studied LBD causality in isolation of other disciplines. The underlying assumption is that each discipline can fully explain causality and each discipline is treated as if it were mutually exclusive and exhaustive of the other disciplines. Hence, the body of knowledge has progressed along research silos where we have in-depth knowledge along given research tracks that are defined by the boundaries of the discipline. Furthermore, a wealth of knowledge has been amassed within each of these research silos. How can they all be correct if they are indeed mutually exclusive and exhaustive? The answer is: they cannot be. This brief review of the state-of-the art in LBD research applied to ergonomics, suggests that instead of observing LBD through the myopic lens of each discipline, we need to begin to view LBD causality as a system. Recent work attempting to understand the interaction between these traditional disciplines has demonstrated that many of the findings along these silos are really interrelated and can be explained in terms of changes in the biomechanical loading at the tissue level. It is argued that further efforts to understand these interactions represent the next level of understanding causality of LBDs.

Causality↗

Molecular polymorphism of the intermediate filament protein transitin.

Transitin is an avian intermediate filament protein whose transient expression in the progenitor cells of the muscle and nerve tissues is similar to that of mammalian nestin. Both proteins contain an alpha-helical core domain flanked by a short N-terminal head and a long C-terminal extremity. However, the tail region of transitin is significantly different from that of nestin in that it harbors a unique motif containing more than 50 leucine zipper-like heptad repeats which is not found in any other intermediate filament protein. Despite the absence of introns in this region of the transitin gene, it was reported that different isoforms of the protein were produced by exclusion or inclusion of a number of repeats generated by an unusual splicing mechanism recognizing consensus 5' and 3' splice sites contained within the coding sequence of the heptad repeat domain [Napier et al. (1999) J Mol Neurosci 12:11-22]. Two monoclonal antibodies (mAbs) reacting with repeated epitopes of this motif were used to monitor transitin expression during in vitro myogenesis of the quail myogenic cell line QM7. Confocal microscopy revealed that the subcellular domains decorated with mAbs A2B11 and VAP-5 were mutually exclusive: the intermediate filament network visualized with mAb VAP-5 appeared to abut on a submembranous domain defined by mAb A2B11. When QM7 cells were induced to differentiate by switching to medium containing low serum components, an early effect was the local loss of A2B11 cortical staining at the points of cell-cell contacts. The A2B11 signal also disappeared before that of VAP-5 in newly formed myotubes. Unexpectedly, the mutually exclusive staining pattern of the mAbs could not be explained by alternative splicing since both epitopes mapped to a repeated element preceding the consensus 5' splice sites of the heptad repeat domain. An alternative explanation would be that the central repeat domain of transitin is a polymorphic structure from which different conformations exist depending on the local context. This hypothesis is strengthened by the observation that in cultured neural crest cells, the A2B11 antigen is preferentially expressed by freely migrating crest cells whose intracellular pH and calcium concentrations are different from those of non-migrating cells.

Amino Acid Sequence↗

A comparison of service use and costs among adults with ADHD and adults with other chronic diseases.

OBJECTIVE: This study compared health service use and costs among adults with attention-deficit hyperactivity disorder (ADHD) and adults with depression, diabetes, or seasonal allergic rhinitis (seasonal allergy). METHODS: Pharmacy and medical claims data from January 1, 1999, to December 31, 2001, were obtained from a large U.S. managed care plan. Patients were divided into one of four mutually exclusive cohorts (ADHD, depression, diabetes, or seasonal allergy) on the basis of their diagnosis or prescriptions. Age, gender, comorbid conditions, and type of dominant provider were compared for the four groups. Thereafter, general linear models with post-hoc multiple comparison tests were used to compare health service use and costs by site of service. RESULTS: The study population included 143,561 patients. The four mutually exclusive groups included 58,017 with depression, 45,479 with diabetes, 33,272 with a seasonal allergy, and 6,793 had ADHD. Comorbid mental health conditions occurred with significantly greater frequency among patients with ADHD and among those with depression than among patients in the other groups. Patients with ADHD and those with depression received care from a mental health provider significantly more often than those with diabetes or a seasonal allergy. Patients with ADHD had fewer average outpatient, inpatient, and emergency department visits than patients with depression or diabetes, and office visit frequency for patients with ADHD was significantly different from that of patients with a seasonal allergy. Annual total costs were lowest among patients with a seasonal allergy ($2,743), which were not significantly different than the costs for patients with ADHD ($3,020). CONCLUSIONS: Adult ADHD poses an economic burden that is less than that of depression or diabetes but greater than that of a seasonal allergy.

Adult↗

Depletion of the co-chaperone CDC-37 reveals two modes of PAR-6 cortical association in C. elegans embryos.

PAR proteins play roles in the establishment and maintenance of polarity in many different cell types in metazoans. In C. elegans, polarity established in the one-cell embryo determines the anteroposterior axis of the developing animal and is essential to set the identities of the early blastomeres. PAR-1 and PAR-2 colocalize at the posterior cortex of the embryo. PAR-3, PAR-6 and PKC-3 (aPKC) colocalize at the anterior cortex of the embryo. A process of mutual exclusion maintains the anterior and posterior protein domains. We present results indicating that a homolog of the Hsp90 co-chaperone Cdc37 plays a role in dynamic interactions among the PAR proteins. We show that CDC-37 is required for the establishment phase of embryonic polarity; that CDC-37 reduction allows PAR-3-independent cortical accumulation of PAR-6 and PKC-3; and that CDC-37 is required for the mutual exclusion of the anterior and posterior group PAR proteins. Our results indicate that CDC-37 acts in part by maintaining PKC-3 levels and in part by influencing the activity or levels of other client proteins. Loss of the activities of these client proteins reveals that there are two sites for PAR-6 cortical association, one dependent on CDC-42 and not associated with PAR-3, and the other independent of CDC-42 and co-localizing with PAR-3. We propose that, in wild-type embryos, CDC-37-mediated inhibition of the CDC-42-dependent binding site and PAR-3-mediated release of this inhibition provide a key mechanism for the anterior accumulation of PAR-6.

Animals↗

p107 uses a p21CIP1-related domain to bind cyclin/cdk2 and regulate interactions with E2F.

The kinase activities of the cyclin/cdk complexes can be regulated in a number of ways. The most recently discovered mechanism of regulation is the association of cdk inhibitors (CKIs), such as p21, p27, and p57, with these complexes. In this report we demonstrate that the pRB-related protein p107, like the p21 family of cdk inhibitors, can inhibit the phosphorylation of target substrates by cyclin A/cdk2 and cyclin E/cdk2 complexes, and the associations of p107 and p21 with cyclin/cdk2 rely on a structurally and functionally related interaction domain. Furthermore, interactions between p107 or p21 with cyclin/cdk2 complexes are mutually exclusive. In cells treated with DNA-damaging agents elevated levels of p21 cause a dissociation of p107/cyclin/cdk2 complexes to yield p21/cyclin/cdk2 complexes. Finally, the consequences of cyclin/cdk2 interactions with p107 have been examined. The activation of the p107-bound cyclin/cdk kinases leads to dissociation of p107 from the transcription factor E2F. Together, these results suggest that cyclin/cdk complexes can be regulated by protein molecules from different families in a mutually exclusive manner in response to certain signals and that these inhibitory proteins may have a potential role in regulating macromolecular assembly.

Amino Acid Sequence↗

Coding the circumstances of injury: ICD-10 a step forward or backwards?

The International Classification of Diseases (ICD) E codes are the most widely used coding frame for categorising the circumstances of injury and poisoning. In 1992 major revisions to the E codes were released. The aim of this paper was to consider whether the changes made are a step forward or backwards in terms of facilitating injury prevention. The approach taken was to reflect on some former injury prevention research needs and the challenges they presented using data coded according to ICD-9, and then to consider how, if at all, ICD-10 has addressed these difficulties. As with ICD-9, there are essentially two axes associated with each cause: intent and mechanism of injury, and these are captured by one code. This approach can have the unintended effect of hiding the significance of some mechanisms of injury. While there have been significant improvements in some areas, such as falls, in others, such as injuries due to firearms, ICD-10 has taken a step backward. In addition the failure to produce mutually exclusive codes presents problems for determining the incidence of downing events. A welcome addition are "optional" activity codes which enable the identification of work related and sport related injury for the first time. Nevertheless, the limited range of codes and absence of coding guides limits their utility. The revised place of occurrence codes do not represent a significant improvement on ICD-9 in that they are limited to 10, they are not mutually exclusive, and they do not adequately cover a range of specific places of occurrence. In summary, relative to its predecessor, ICD-10 represents a significant improvement in many areas. Unfortunately, it still falls far short of the mark for many injury prevention needs.

Accidental Falls↗

Distinct pools of proliferating cell nuclear antigen associated to DNA replication sites interact with the p125 subunit of DNA polymerase delta or DNA ligase I.

Proliferating cell nuclear antigen (PCNA) plays an essential role in DNA replication, repair, and cell cycle control. PCNA is a homotrimeric ring that, when encircling DNA, is not easily extractable. Consequently, the dynamics of protein-protein interactions established by PCNA at DNA replication sites is not well understood. We have used DNase I to release DNA-bound PCNA together with replication proteins including the p125-catalytic subunit of DNA polymerase delta (p125-pol delta), DNA ligase I, cyclin A, and cyclin-dependent kinase 2 (CDK2). Interaction with these proteins was investigated by immunoprecipitation with antibodies binding near the interdomain connector loop or to the C-terminal domain of PCNA, respectively, or with antibodies to p125-pol delta or DNA ligase I. PCNA interaction with p125-pol delta or DNA ligase I was detected only by the latter antibodies, and found to be mutually exclusive. In contrast, antibodies to PCNA co-immunoprecipitated only CDK2. A GST-p21(waf1/cip1) C-terminal peptide displaced p125-pol delta and DNA ligase I, but not CDK2, from PCNA. These results suggest that PCNA trimers bound to DNA during the S phase are organized as distinct pools able to bind selectively different partners. Among them, p125-pol delta and DNA ligase I interact with PCNA in a mutually exclusive manner.

Antibodies↗

Directional binding of HMG-I(Y) on four-way junction DNA and the molecular basis for competitive binding with HMG-1 and histone H1.

Histone H1, HMG-1 and HMG-I(Y) are mammalian nuclear proteins possessing distinctive DNA-binding domain structures that share the common property of preferentially binding to four-way junction (4H) DNA, an in vitro mimic of the in vivo genetic recombination intermediate known as the Holliday junction. Nevertheless, these three proteins bind to 4H DNA in vitro with very different affinities and in a mutually exclusive manner. To investigate the molecular basis for these distinctive binding characteristics, we employed base pair resolution hydroxyl radical footprinting to determine the precise sites of nucleotide interactions of both HMG-1 and histone H1 on 4H DNA and compared these contacts with those previously described for HMG-I(Y) on the same substrate. Each of these proteins had a unique binding pattern on 4H DNA and yet shared certain common nucleotide contacts on the arms of the 4H DNA molecule near the branch point. Both the HMG-I(Y) and HMG-1 proteins made specific contacts across the 4H DNA branch point, as well as interacting at discrete sites on the arms, whereas the globular domain of histone H1 bound exclusively to the arms of the 4H DNA substrate without contacting nucleotides at the crossover region. Experiments employing the chemical cleavage reagent 1, 10-orthophenanthroline copper(II) attached to the C-terminal end of a site-specifically mutagenized HMG-I(Y) protein molecule demonstrated that this protein binds to 4H DNA in a distinctly polar, direction-specific manner. Together these results provide an attractive molecular explanation for the observed mutually exclusive 4H DNA-binding characteristics of these proteins and also allow for critical assessment of proposed models for their interaction with 4H DNA substrates. The results also have important implications concerning the possible in vivo roles of HMG-I(Y), histone H1 and HMG-1 in biological processes such as genetic recombination and retroviral integration.

Animals↗

An enhancer directs differential expression of the linked Mrf4 and Myf5 myogenic regulatory genes in the mouse.

The myogenic regulatory factors, Mrf4 and Myf5, play a key role in skeletal muscle formation. An enhancer trap approach, devised to isolate positive-acting elements from a 200-kb YAC covering the mouse Mrf4-Myf5 locus in a C2 myoblast assay, yielded an enhancer, A17, which mapped at -8 kb 5' of Mrf4 and -17 kb 5' of Myf5. An E-box bound by complexes containing the USF transcription factor is critical for enhancer activity. In transgenic mice, A17 gave two distinct and mutually exclusive expression profiles before birth, which correspond to two phases of Mrf4 transcription. Linked to the Tk or Mrf4 minimal promoters, the nlacZ reporter was expressed either in embryonic myotomes, or later in fetal muscle, with the majority of Mrf4 lines showing embryonic expression. When linked to the Myf5 minimal promoter, only fetal muscle expression was detected. These observations identify A17 as a sequence that targets sites of myogenesis in vivo and raise questions about the mutually exclusive modes of expression and possible promoter/enhancer interactions at the Mrf4-Myf5 locus.

Animals↗

A definition of bias founded on the concept of the study base.

We propose a definition of bias founded on the concept of the study base. The definition is unrelated to the study design, thereby permitting a clear comparison of validity among different study types. Also, it facilitates assessment of bias because it allows bias to be subdivided under mutually exclusive categories. In relation to the study base, the epidemiologic study can be viewed as involving three distinct steps. First, the person-time (study base) is specified for the study. Second, the investigators collect data on disease events and person-time among the exposed and unexposed from the study base. Third, they calculate an estimate of the effect of the exposure using the data. Categories pertaining to each of these three steps will create mutually exclusive categories of bias. We suggest the following terminology: the first step generates confounding, the second results in misclassification and misrepresentation, and the third produces analysis deviation. The total bias is the sum of the confounding, misclassification, misrepresentation, and analysis deviation. We illustrate our proposed epidemiologic theory with examples from various biological settings.

Bias↗