Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

Background

The immune system has paradoxical roles during cancer development and the prognostic significance of immune modulating factors is controversial. The aim of this study was to determine the expression of cyclooxygenase 2 (COX-2), transforming growth factor-beta (TGF- beta), interleukin-10 (IL-10) and their prognostic significance in breast cancers. Ki67 was included as a measure of growth fraction of tumor cells.

Methods

On immunohistochemical stained slides from 38 breast cancer patients, we performed digital video analysis of tumor cell areas and adjacent tumor stromal areas from the primary tumors and their corresponding lymph node metastases. COX-2 was recorded as graded staining intensity.

Results

The expression of TGF-beta, IL-10 and Ki67 were recorded in tumor cell areas and adjacent tumor stromal areas. In both primary tumors and metastases, the expression of COX-2 was higher in the tumor stromal areas than in the tumor cell areas (both P < 0.001). High stromal staining intensity in the primary tumors was associated with a 3.9 (95% CI 1.1-14.2) times higher risk of death compared to the low staining group (P = 0.036). The expression of TGF-beta was highest in the tumor cell areas of both primary tumors and metastases (both P < 0.001). High stromal expression of TGF-beta was associated with increased mortality. For IL-10, the stromal expression was highest in the primary tumors (P < 0.001), whereas in the metastases the expression was highest in tumor cell areas (P < 0.001). High IL-10 expression in tumor- and stromal cell areas of primary tumors predicted mortality. Ki67 was higher expressed in tumor stromal areas of the metastases, and in tumor cell areas of the primary tumors (P < 0.001). Ki67 expression in tumor cell areas and stromal areas of the metastases was independently associated with breast cancer mortality.

Conclusions

Stromal expression of COX-2, TGF-beta and Ki67 may facilitate tumor progression in breast cancer.     

Effect of estrogen on radiation-induced cataractogenesis

Cataractogenesis is a widely reported late effect that is observed in patients receiving total-body irradiation (TBI) prior to bone marrow transplantation or radiotherapy for ocular or head and neck cancers. Recent studies indicate that estrogens may protect against age-related and drug-induced cataracts. Moreover, other reports suggest that estrogen possesses antioxidant properties. Since the effect of estrogen on radiation cataractogenesis is unknown, we wished to determine whether estrogen modulates radiation-induced opacification of the lens. Intact or ovariectomized Sprague-Dawley rats were treated with either 17-beta-estradiol or an empty silastic capsule. The right orbit was then irradiated with either 10 or 15 Gy of (60)Co gamma rays using a Leksell Gamma Knife, and lenses were examined at various times postirradiation with a slit lamp or evaluated for light transmission. We found that for ovariectomized rats irradiated with 15 Gy, the lens opacity and the incidence of cataract formation in the estradiol-treated group were significantly increased compared to the control group at the end of the 25-week period of observation. Cataract incidence was also high in irradiated eyes of ovary-intact animals at 25 weeks postirradiation but was greatly reduced in the ovariectomized control group, with less than half of irradiated eyes showing evidence of cataractogenesis. Thus, after irradiation with 15 Gy of gamma rays, estrogen increased the incidence of cataract formation. We also observed that although the incidence of cataract formation in rats irradiated with 10 Gy and receiving continuous estrogen treatment was not altered compared to rats in the control group that did not receive estrogen, the latent period for posterior subcapsular cataract formation decreased and the severity of the anterior cataract increased. Taken together, our data suggest that estrogen accelerates progression of radiation-induced opacification.     

The Forgotten Component of Plant Water Potential: A Reply - Tissue Pressures are not Additive in the Way M. J. Canny Suggests

Abstract: Martin Canny's concepts of "tissue pressure" and its derivative "compensating pressure" are reviewed. Tissue pressure arises when the volume change of some living cells exerts a pressure on adjacent living or dead cells. Contrary to previous assertions, tissue pressure cannot cause a permanent change in pressure potential or water potential of adjacent cells. Tissue pressure induces only a transitory increase of pressure and water potential. After equilibrium is reestablished, the same or a more negative pressure or water potential results. The idea that tissue pressure can prevent or repair xylem embolism is without merit.     

Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected vertebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic results compared with a well-established tree based on both morphological and molecular data. The best results (the greatest level of support of well-accepted nodes) were obtained when the complete data set was used. However, some previously supported nodes were resolved using either the stem or loop bases alone. Stem bases sustain a greater number of compensatory mutations than would be expected at random, but the number is < 40% of that expected under a hypothesis of perfect compensation to maintain secondary structure. Therefore, we suggest that in phylogenetic analyses, the weighting of stem characters be reduced by no more than 20%, relative to that of loop characters. In contrast to previous suggestions, we do not recommend weighting of stem positions by one-half, compared with that of loop positions, because this overcompensates for the constraints that selection imposes on the secondary structure of rRNA.      

Maple sap uptake, exudation, and pressure changes correlated with freezing exotherms and thawing endotherms

Sap flow rates and sap pressure changes were measured in dormant sugar maple trees (Acer saccharum Marsh.). In the forest, sap flow rates and pressure changes were measured from tap holes drilled into tree trunks in mature trees and sap flow rates were measured from the base of excised branches. Excised branches were also brought into the laboratory where air temperature could be carefully controlled in a refrigerated box and sap flow rates and sap pressures were measured from the cut base of the branches.

Under both forest and laboratory conditions, sap uptake occurred as the wood temperature declined but much more rapid sap uptake correlated with the onset of the freezing exotherm. When sap pressures were measured under conditions of negligible volume displacement, the sap pressure rapidly fell to −60 to −80 kilopascals at the start of the freezing exotherm. The volume of water uptake and the rate of uptake depended on the rate of freezing. A slow freezing rate correlated with a large volume of water uptake, a fast freezing rate induced a smaller volume of water uptake. The volume of water uptake ranged from 0.02 to 0.055 grams water per gram dry weight of sapwood. The volume of water exuded after thawing was usually less than the volume of uptake so that after several freezing and thawing cycles the sapwood water content increased from 0.7 to 0.8 grams water per gram dry weight.

These results are discussed in terms of a physical model of the mechanism of maple sap uptake and exudation first proposed by P. E. R. O'Malley. The proposed mechanism of sap uptake is by vapor distillation in air filled wood fiber lumina during the freezing of minor branches. Gravity and pressurized air bubbles (compressed during freezing) cause sap flow from the canopy down the tree after the thaw.

     

Effect of stem water content on sap flow from dormant maple and butternut stems: induction of sap flow in butternut

Sap flow from excised maple stems collected over the winter (1986/87) was correlated with stem water content. Stem water content was high in the fall (>0.80) and decreased rapidly during 2 weeks of continuous freezing temperatures in late winter (<0.60). Exudation of sap from stem segments subjected to freeze/thaw cycles was small (<10 mL/kg) in the fall, but substantial exudation (45-50 mL/kg) occurred following the decline in water content. These observations are consistent with Milburn's and O'Malley's models (J.A. Milburn, P.E.R. O'Malley [1984] Can J Bot 62: 2101-2106; P.E.R. O'Malley, J.A. Milburn [1983] Can J Bot 61:3100-3106) of sap absorption into gas-filled fibers during freezing. Exudation volume was increased 200 to 300% in maple stems originally at high water content (>0.80) after perfusion with sucrose and dehydration at −12°C. Sap flow was also induced in butternut stem segments after the same treatment. Thus, sap flow may not be unique to maples. Sap flow could not be increased in stem segments dehydrated at 4°C. Migration of water molecules from small ice crystals in fibers to larger crystals in vessels while stems were frozen may account for increase exudation after dehydration at −12°C. This would result in preferential dehydration of fibers and a distribution of gas and sap favorable for stem-based sap flow.     

Use of positive pressures to establish vulnerability curves : further support for the air-seeding hypothesis and implications for pressure-volume analysis

Loss of hydraulic conductivity occurs in stems when the water in xylem conduits is subjected to sufficiently negative pressure. According to the air-seeding hypothesis, this loss of conductivity occurs when air bubbles are sucked into water-filled conduits through micropores adjacent to air spaces in the stem. Results in this study showed that loss of hydraulic conductivity occurred in stem segments pressurized in a pressure chamber while the xylem water was under positive pressure. Vulnerability curves can be defined as a plot of percentage loss of hydraulic conductivity versus the pressure difference between xylem water and the outside air inducing the loss of conductivity. Vulnerability curves were similar whether loss of conductivity was induced by lowering the xylem water pressure or by raising the external air pressure. These results are consistent with the air-seeding hypothesis of how embolisms are nucleated, but not with the nucleation of embolisms at hydrophobic cracks because the latter requires negative xylem water pressure. The results also call into question some basic underlying assumptions used in the determination of components of tissue water potential using “pressure-volume” analysis.     

Identification of the precursor protein to basement membrane heparan sulfate proteoglycans

The precursor protein of a basement membrane specific heparan sulfate proteoglycan has been identified as a 400,000 Mr polypeptide. Antibodies against large and small forms of this proteoglycan, isolated from a basement membrane (Engelbreth-Holm-Swarm, EHS) tumor, immunoprecipitated the same 400,000 protein from pulse-labeled EHS cells. The proteoglycan precursor protein was not recognized by antibodies against other basement membrane components or by antibodies to the cartilage proteoglycan. Furthermore, heparan sulfate proteoglycan purified from the EHS tumor blocked the immunoprecipitation of the precursor protein. Pulse-chase studies with [35S]methionine showed the precursor protein was converted to a proteoglycan. Pulse-chase studies with 35SO4 showed the large, low density proteoglycan appeared first and was degraded to a smaller, high density proteoglycan. We propose that the precursor protein is used after very little or no modification in the assembly of a large, low density heparan sulfate proteoglycan and that a portion of the population of these macromolecules are subsequently degraded to a smaller form.     

Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models

Background  

With the explosion of microarray studies, an enormous amount of data is being produced. Systematic integration of gene expression data from different sources increases statistical power of detecting differentially expressed genes and allows assessment of heterogeneity. The challenge, however, is in designing and implementing efficient analytic methodologies for combination of data generated by different research groups.