Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites

Polypurine tracts are important elements of eukaryotic promoters. They are believed to somehow destabilize chromatin, but the mechanism of their action is not known. We show that incorporating an A(16) element at an end of the nucleosomal DNA and further inward destabilizes histone-DNA interactions by 0.1 +/- 0.03 and 0.35 +/- 0.04 kcal mol(-1), respectively, and is accompanied by 1.5- +/- 0.1-fold and 1.7- +/- 0.1-fold increases in position-averaged equilibrium accessibility of nucleosomal DNA target sites. These effects are comparable in magnitude to effects of A(16) elements that correlate with transcription in vivo, suggesting that our system may capture most of their physiological role. These results point to two distinct but interrelated models for the mechanism of action of polypurine tract promoter elements in vivo. Given a nucleosome positioned over a promoter region, the presence of a polypurine tract in that nucleosome's DNA decreases the stability of the DNA wrapping, increasing the equilibrium accessibility of other DNA target sites buried inside that nucleosome. Alternatively (if nucleosomes are freely mobile), the presence of a polypurine tract provides a free energy bias for the nucleosome to move to alternative locations, thereby changing the equilibrium accessibilities of other nearby DNA target sites.

Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites

Posttranslational acetylation of the conserved core histone N-terminal tail domains is linked to gene activation, but the molecular mechanisms involved are not known. In an earlier study we showed that removing the tail domains altogether by trypsin proteolysis (which leaves nucleosomes nevertheless intact) leads to 1.5 to 14-fold increases in the dynamic equilibrium accessibility of nucleosomal DNA target sites. These observations suggested that, by modestly increasing the equilibrium accessibility of buried DNA target sites, histone acetylation could result in an increased occupancy by regulatory proteins, ultimately increasing the probability of transcription initiation. Here, we extend these observations to a more natural system involving intact but hyperacetylated nucleosomes. We find that histone hyperacetylation leads to 1.1 to 1.8-fold increases in position-dependent equilibrium constants for exposure of nucleosomal DNA target sites, with an average increase of 1.4(+/-0.1)-fold. The mechanistic and biological implications of these results are discussed.

Patients with reconstruction of craniofacial or intraoral defects: development of instruments to measure quality of life

Patients with reconstruction of craniofacial or intraoral defects experience a profound impact on their quality of life (QOL). This impact on QOL is influenced by the patients' medical conditions and the treatment interventions. Instruments to measure general QOL have been available for many years. A major criticism of QOL instruments is that too often the questions are not specific to the particular problems of a disease or condition. A search of the literature regarding QOL measurement for patients with maxillofacial implant-supported prostheses produced a short list of instruments, none of which were sufficiently developed or suited to the patients involved in reconstructive treatment. This study was designed to develop pretreatment and posttreatment questionnaires for measuring QOL for patients with reconstruction of a craniofacial defect and patients with reconstruction of loss of specific intraoral structures utilizing an implant-supported prosthesis (e.g., severe resorption of the maxilla or mandible or both). The goal was to develop brief, targeted instruments for this specific patient population. The produced instruments were sensitive and easy to administer and score, and no disruption of clinical care occurred with the administration of the questionnaires. The instruments were used with equal success both in face-to-face interviews and via mail.

Nep1 Protein from Fusarium oxysporum Enhances Biological Control of Opium Poppy by Pleospora papaveracea

ABSTRACT The fungus Pleospora papaveracea and Nep1, a phytotoxic protein from Fusarium oxysporum, were evaluated for their biocontrol potential on opium poppy (Papaver somniferum). Four treatments consisting of a control, P. papaveracea conidia, Nep1 (5 mug/ml), and P. papaveracea conidia plus Nep1 (5 mug/ml) were used in detached-leaf and whole-plant studies. Conidia of P. papaveracea remained viable for 38 days when stored at 20 or 4 degrees C. Nep1 was stable in the presence of conidia for 38 days when stored at 4 degrees C or for 28 days at 20 degrees C. The presence of Nep1 did not affect conidia germination or appressoria formation. Nep1 was recovered from drops applied to opium poppy leaves in greenhouse and field studies 24 h after treatment. Opium poppy treated with the combination of Nep1 and P. papaveracea had higher necrosis ratings than the other treatments. There were changes in the intercellular protein profiles, determined by sodium dodecyl sulfate gel electrophoresis and silver staining, due to application of treatments; the most intense occurred in response to the combination of Nep1 and P. papaveracea. The combination of Nep1 and P. papaveracea enhanced the damage caused to opium poppy more than either component alone.

Evaluation of Infection Processes and Resulting Disease Caused by Dendryphion penicillatum and Pleospora papaveracea on Papaver somniferum

ABSTRACT Two pathogenic fungi of opium poppy, Pleospora papaveracea and Dendryphion penicillatum, were isolated from field material in Beltsville, MD. The processes of infection by these two fungi were studied to determine the optimal environmental conditions for infection. Both fungi formed appressoria capable of penetrating directly through the plant epidermal layer. Of the two fungi, P. papaveracea was more aggressive, causing more rapid necrosis. Appressorial formation by P. papaveracea occurred as early as 4 h after application of a conidial suspension to poppy leaves. P. papaveracea formed more appressoria than did D. penicillatum, especially at cool temperatures (7 to 13 degrees C). In greenhouse studies, P. papaveracea caused more damage to opium poppy than did D. penicillatum when applied in 10% unrefined corn oil. In the field, P. papaveracea was more consistent in its effects on opium poppy from a local seed source designated Indian Grocery. P. papaveracea caused higher disease ratings, more stem lesions, and equal or greater yield losses than did D. penicillatum on Indian Grocery. The late-maturing opium poppy variety White Cloud was severely damaged by disease, regardless of formulation or fungal treatment. P. papaveracea was the predominant fungus isolated from poppy seed capsules and the only fungus reisolated from the field the following year. These studies provide a better understanding of the infection process and the differences between these two pathogenic fungi and will be beneficial for the development of the fungi as biological control agents.

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

We have previously shown that nucleosomes are conformationally dynamic: DNA sequences that in the time-average are buried inside nucleosomes are nevertheless transiently accessible, even to large proteins (or any other macromolecule). We refer to this dynamic behavior as "site exposure". Here we show that: (i) the equilibrium constants describing this dynamic site exposure decrease progressively from either end of the nucleosomal DNA in toward the middle; and (ii) these position-dependent equilibrium constants are strongly dependent on the nucleosomal DNA sequence. The progressive decrease in equilibrium constant with distance inside the nucleosome supports the hypothesis that access to sites internal to a nucleosome is provided by progressive (transient) release of DNA from the octamer surface, starting from one end of the nucleosomal DNA. The dependence on genomic DNA sequence implies that a specific genomic DNA sequence could be a major determinant of target site occupancies achieved by regulatory proteins in vivo, by either governing the time-averaged accessibility for a given nucleosome position, or biasing the time-averaged positioning (of mobile nucleosomes), which in turn is a major determinant of site accessibility.

Phenotypic mapping of human mesothelial cells

In recent years it has become clear that the mesothelium plays a prominent homeostatic role in the peritoneum, and can be profoundly altered in disease and during peritoneal dialysis. The cell-surface phenotype of the mesothelial cell has not been thoroughly investigated. This study begins to identify cell surface molecules which may be important in mesothelial functions such as adhesion and interaction with cells of the immune system. The expression of adhesion structures on mesothelial cells such as CD44, the beta integrin chain CD29, the beta 3 integrin chain CD61 and alpha chains CD49 alpha (alpha 1), CD49b (alpha 2), CD49c (alpha 3), CD49e (alpha 5), and CD51 (alpha v) is described. In addition, a wide range of novel molecules including CD90, CD105, CD140b, CD142, CD147, CD151, CD157, CD165, and CD166 are identified. The role and function of such molecules in mesothelial biology and their significance for peritoneal dialysis is discussed.

Need for evidence-based practice in prosthodontics

STATEMENT OF PROBLEM

Patients, their insurers, the courts, and the scientific community are demanding more evidence to support the effectiveness of health care strategies.

PURPOSE

This article describes evidence-based practice, its origins, and value as a way of addressing the demand for evidence of treatment effectiveness in maxillofacial prosthetics.

MATERIAL AND METHODS

A limited review of maxillofacial prosthetics literature was performed using Medline over the years 1966 to 1998. The retrieved articles were classified by methodologic design and assessed for the strength of their evidence.

RESULTS

Focused and speedy (but not necessarily comprehensive) literature searching methods are available. Critical appraisal skills are available and needed to assess the quality of evidence in support of a treatment and to maintain clinical skills.

CONCLUSION

With appropriate skills and the availability of literature searching hardware and software, evidence-based practice is a powerful means for the practitioner to establish the effectiveness of individual patient treatment, and to prevent the diminution of clinical skills over the course of a career. These skills should be included in training programs.

Europa's differentiated internal structure: inferences from four Galileo encounters

Radio Doppler data from four encounters of the Galileo spacecraft with the jovian moon Europa have been used to refine models of Europa's interior. Europa is most likely differentiated into a metallic core surrounded by a rock mantle and a water ice-liquid outer shell, but the data cannot eliminate the possibility of a uniform mixture of dense silicate and metal beneath the water ice-liquid shell. The size of a metallic core is uncertain because of its unknown composition, but it could be as large as about 50 percent of Europa's radius. The thickness of Europa's outer shell of water ice-liquid must lie in the range of about 80 to 170 kilometers.

Distribution of rock, metals, and ices in Callisto

Radio Doppler data from a single encounter (C3) of the Galileo spacecraft with Callisto, the outermost Galilean moon of Jupiter, indicated that Callisto was probably undifferentiated. Now, similar data from a second encounter (C9) corroborate this conclusion, but more accurate data from a third encounter (C10) indicate that the rock and ice within Callisto have partially, but not completely, separated. Callisto may be differentiated into a rock-metal core less than 25 percent of Callisto's radius, an outer layer of clean ice less than 350 km thick, and a middle layer of mixed rock and ice. Models in which ice and rock are mixed all the way to the center of Callisto are also consistent with the data.

The need for criteria on reporting treatment outcomes

Early reports that established the success of osseointegration and the survival of implants or prostheses measured the outcome in a number of case series studies. From the standpoint of scientific rigor, the case series design is among the weakest available. Patients have reported that they are better off basing their judgment on their own values and experiences. It is unlikely that they use implant or prosthesis survival as their only measures. This article examines the existing measures within a classification, the problems with developing relevant new measures, and reviews some desirable outcome measures attributes.

A pulsar, the heliosphere, and pioneer 10: probable mimicking of a planet of PSR B1257+12 by solar rotation

Doppler data generated with the Pioneer 10 spacecraft's radio carrier wave between 1987 and 1995 show a 25.3-day periodicity which is related to the solar rotation. The timing data of the pulsar PSR B1257+12 also show a periodicity of 25.34 days, which has been explained as a signature of the pulsar's barycentric motion in response to the existence of a small moon-like object. However, because PSR B1257+12 is located close to the ecliptic and because the timing variations are in the range of microseconds, it is likely that the pulsar signal is affected by the same mechanism acting on the Pioneer 10 Doppler data. Hence, the hypothesized inner planet around PSR B1257+12 is probably an artifact of the heliosphere.

Europa's differentiated internal structure: inferences from two Galileo encounters

Doppler data generated with the Galileo spacecraft's radio carrier wave during two Europa encounters on 19 December 1996 (E4) and 20 February 1997 (E6) were used to measure Europa's external gravitational field. The measurements indicate that Europa has a predominantly water ice-liquid outer shell about 100 to 200 kilometers thick and a deep interior with a density in excess of about 4000 kilograms per cubic meter. The deep interior could be a mixture of metal and rock or it could consist of a metal core with a radius about 40 percent of Europa's radius surrounded by a rock mantle with a density of 3000 to 3500 kilograms per cubic meter. The metallic core is favored if Europa has a magnetic field.

Gravitational evidence for an undifferentiated Callisto

Before the arrival of the Galileo spacecraft at Jupiter, models for the interior structure of the four galilean satellites--Io, Europa, Ganymede and Callisto-ranged from uniform mixtures of rock and ice (that is, undifferentiated objects) or rocky cores surrounded by a mantle of water ice. Now it appears that Io has a large metallic core and that Ganymede is strongly differentiated, most probably into a three-layer structure consisting of a metallic core, a silicate mantle and a deep outer layer of ice. Direct information on the interior structure of Callisto determined from previous spacecraft fly-bys was essentially limited to an estimate of the mean density being intermediate between pure ice and pure rock. Here we report measurements of Callisto's gravitational field which reveal that, in contrast to Io and Ganymede, this galilean satellite is most probably a homogeneous object consisting of a solar mixture of 40% compressed ice and 60% rock (including iron and iron sulphide). Callisto's undifferentiated state is consistent with the apparent lack of an intrinsic magnetic field, and indicates that the outermost galilean satellite has not experienced a heating phase sufficiently high to separate its rock and metal components from the lighter ices.

The 24-kDa protein from Fusarium oxysporum f.sp. erythroxyli: occurrence in related fungi and the effect of growth medium on its production

A 24-kDa protein that elicits ethylene production and necrosis in leaves of dicotyledonous plants was previously purified from culture filtrates of Fusarium oxysporum Schlechtend:Fr. f.sp. erythroxyli. Antisera to the denatured 24-kDa protein detected 2.5 ng of the 24-kDa protein on Western blots at 100000-fold dilutions. The antisera cross-reacted with a 24-kDa protein on Western blots of culture filtrates from three other F. oxysporum formae speciales. Of seven Fusarium species, only F. oxysporum, F. acuminatum Ellis and Kellerm., and F. avenaceum (Fr.:Fr.) Sacc. isolates produced an antigenically related 24-kDa protein. Although there were differences in the profiles of proteins extracted from stems of coca (Erythroxylum coca var. coca L. Lam.) infected with F. oxysporum f.sp. erythroxyli compared with uninfected stems, antisera to the 24-kDa protein did not cross-react with any proteins from the infected coca stems. For the fungal isolates studied, the best medium tested for production of the 24-kDa protein contained 1% sucrose and 1% asparagine. Biological activity of the F. oxysporum culture filtrates on sweet basil leaves was consistently correlated with the presence of the 24-kDa protein. Production of the 24-kDa protein was limited in cultures containing pectin or cellulose as the primary carbon source, or in cultures lacking sucrose or casamino acids. Water-soluble extracts from coca stems inhibited production of the 24-kDa protein, whereas cellulose and pectin did not. Components produced by the plant may limit production of the 24-kDa protein in infected plant tissue and thereby limit the response of the plant to the fungus. These results suggest the 24-kDa protein does not function in the symptomatic phase of the F. oxysporum f.sp. erythroxylicoca disease interaction.