Sulindac enhances cell proliferation in DMH-treated mouse colonic mucosa

In a previous study we reported that the NSAID sulindac had a marked inhibitory effect on the development of colonic tumours in mice treated with the carcinogen 1,2-dimethylhydrazine (DMH). In this study we examined the effects of sulindac in respect of cell-kinetic changes in mouse colonic mucosa as determined by flash labelling with the thymidine analogue bromodeoxyuridine (BrdUrd) at varying intervals during the process of colonic carcinogenesis. We also investigated the possibility that these changes may be modulated by misoprostol a prostaglandin E₁ analogue. Four groups of 36 mice each were treated for 18 weeks with the following drug/s respectively: (1) DMH; (2) DMH and sulindac; (3) DMH, sulindac and misoprostol; and (4) DMH and misoprostol. Three animals from each group were killed each week between the sixth week and the eighteenth week after the start of the experiment. A 1-h flash label technique was employed and paraffin sections of colonic mucosa were examined. For each animal a total of 50 perfect axially cut crypts were chosen and the following parameters determined: crypt length, labelling index and labelling index distribution: the data were analysed using the computer program GLIM. For each of the four groups, crypt lengths increased significantly with the duration of treatment with no significant difference between the groups. In sulindac-treated animals the labelling index for all positions increased with duration of treatment whereas for animals not treated with sulindac there was no significant difference in labelling index with respect to duration of treatment. The administration of misoprostol did not appear to significantly alter the effects of sulindac. It is postulated that the observed increase in cell proliferation could be a compensatory phenomenon occurring secondary to loss of crypt epithelial cells by apoptosis induced by sulindac. Also the finding of an increase in labelling index mediated by a chemopreventive agent indirectly questions the rationale behind the therapeutic manipulation of crypt cell proliferation in order to reduce the risk of colon cancer.     

Neutrophil degranulation detected by right angle light scattering: spectroscopic methods suitable for simultaneous analyses of degranulation or shape change, elastase release, and cell aggregation

We have used simultaneous spectrometric analysis of right angle scattering and elastase release from human neutrophils to demonstrate the similarity of these two measures of degranulation. Both responses depend on the presence of cytochalasin B, and are similar in kinetics, dose-response, and dependence on receptor occupancy at the formyl peptide receptor. This scattering response is shown to be largely independent of cell aggregation. In the absence of cytochalasin B, a rapid and transient right angle scatter response of a different character, probably associated with cell ruffling, is detected. Either right angle response can be detected by flow cytometry.     

Solvent effects on the structure,dynamics and activity of lysozyme

Kuntz and Kauzmann have argued that dehydrating a protein results in conformational changes. In contrast, Rupleyet al. have developed a hydration model which involves no significant change in conformation; the onset of enzyme activity in hen egg-white lysozyme at hydration values of about 0.2 g water/g protein they ascribe rather to a solvation effect. Using a direct difference infra-red technique we can follow specific hydration events as water is added to a dry protein. Conformational studies of lysozyme using laser Raman spectroscopy indicate changes in conformation with hydration that are complete just before measurable activity is found. Parallel nuclear magnetic resonance measurements of exchangeability of the main chain amide hydrogens, as a function of hydration from near dryness, suggest a hydration-related increase in conformational flexibility which occurs before-and is probably necessary for-the Raman-detected conformational changes. Very recent inelastic neutron scattering measurements provides direct evidence of a flexibility change induced by hydration, which is apparently necessary before the enzyme can achieve adequate flexibility for it to begin to function.     

An In Vitro Model for Measuring Immune Responses to Malaria in the Context of HIV Co-infection

Malaria and HIV co-infection is a growing health priority. However, most research on malaria or HIV currently focuses on each infection individually. Although understanding the disease dynamics for each of these pathogens independently is vital, it is also important that the interactions between these pathogens are investigated and understood. We have developed a versatile in vitro model of HIV-malaria co-infection to study host immune responses to malaria in the context of HIV infection. Our model allows the study of secreted factors in cellular supernatants, cell surface and intracellular protein markers, as well as RNA expression levels. The experimental design and methods used limit variability and promote data reliability and reproducibility. All pathogens used in this model are natural human pathogens (Plasmodium falciparum and HIV-1), and all infected cells are naturally infected and used fresh. We use human erythrocytes parasitized with P. falciparum and maintained in continuous in vitro culture. We obtain freshly isolated peripheral blood mononuclear cells from chronically HIV-infected volunteers. Every condition used has an appropriate control (P. falciparum parasitized vs. normal erythrocytes), and every HIV-infected donor has an HIV uninfected control, from which cells are harvested on the same day. This model provides a realistic environment to study the interactions between malaria parasites and human immune cells in the context of HIV infection.     

Volume occupation, environment and accessibility in proteins. The problem of the protein surface.

The volumes occupied by atoms or groups of atoms in ribonuclease S are calculated, using a new treatment of the surface, and considering buried and exposed atoms separately. The volumes occupied by particular atom types fall within a narrow range, with standard deviations between 10% and 15% of the mean. Summation of volumes over main and side-chain groups removes inaccuracies in the single atom data, and results in even narrower distributions. Comparison of the volume spreads with those found in model glasses suggests that the remaining variation is unlikely to be much reduced by improving further either the space-subdivision method or the surface treatment. These improved volume distributions might be used as more stringent criteria against which to test trial tertiary structures.The computer program used produces additional information that could be used to investigate quantitatively the possible freedom of movement in different parts of the molecule. It also provides complementary data on environment and surface exposure.     

Paleoceanography of the Gulf of Alaska during the past 15,000 years: Results from diatoms, silicoflagellates, and geochemistry

High-resolution records of diatoms, silicoflagellates, and geochemistry covering the past 15,000 years were studied in three cores from the Gulf of Alaska (GOA). Core EW0408-85JC in an oceanic setting on the Kayak Slope displays a paleoceanographic record similar to that at several locations on the California margin during deglaciation. Biologic productivity as reconstructed using geochemical and microfossil proxies increased abruptly during the Bølling–Alleröd (Bø–Al) warm interval (14.7–12.9 cal ka), declined during the Younger Dryas (YD) cold interval (12.9 to 11.7 cal kyr BP), and rose again during the earliest Holocene. At this site, the record after ~ 11 cal kyr BP is dominated by oceanic diatoms and silicoflagellates, with geochemical proxies displaying more subtle variation.Cores EW0408-66JC in the Yakobi Sea Valley near Cross Sound and EW0408-11JC in the Gulf of Esquibel contain an expanded, composite record along the southeast Alaskan margin. Core 66JC contains a detailed record of the Bø–Al and YD. Diatoms and silicoflagellates indicate that coastal upwelling and biosiliceous productivity were strong during the Bø–Al but declined during the YD. Sea ice-related diatoms increased in abundance during the YD, indicating cooler, but less productive waters.The glacial to biogenic marine sediment transition in core 11JC occurs at 1280 cmbsf (centimeters below sea floor), probably representing rising sea level and deglaciation early in the Bø–Al. Freshwater and sea-ice related diatoms are common in the lower part of the core (Bø–Al and YD), but upwelling-related diatoms and silicoflagellates quickly increased in relative abundance up-core, dominating the record of the past 11,000 years. Low oxygen conditions in the bottom water as reconstructed using geochemical proxies (U and Mo concentration) were most intense between ~ 6.5 and 2.8 cal kyr BP, the beginning of which is coincident with increases in abundance of upwelling-related diatoms.The records from these three cores jointly thus made it possible to reconstruct paleoclimatic and paleoceanographic conditions at high northern Pacific latitudes during the last 15 kyr.     

Discovery Analysis of TCGA Data Reveals Association between Germline Genotype and Survival in Ovarian Cancer Patients

Background

Ovarian cancer remains a significant public health burden, with the highest mortality rate of all the gynecological cancers. This is attributable to the late stage at which the majority of ovarian cancers are diagnosed, coupled with the low and variable response of advanced tumors to standard chemotherapies. To date, clinically useful predictors of treatment response remain lacking. Identifying the genetic determinants of ovarian cancer survival and treatment response is crucial to the development of prognostic biomarkers and personalized therapies that may improve outcomes for the late-stage patients who comprise the majority of cases.

Methods

To identify constitutional genetic variations contributing to ovarian cancer mortality, we systematically investigated associations between germline polymorphisms and ovarian cancer survival using data from The Cancer Genome Atlas Project (TCGA). Using stage-stratified Cox proportional hazards regression, we examined 650,000 SNP loci for association with survival. We additionally examined whether the association of significant SNPs with survival was modified by somatic alterations.

Results

Germline polymorphisms at rs4934282 (AGAP11/C10orf116) and rs1857623 (DNAH14) were associated with stage-adjusted survival ( = 1.12e-07 and 1.80e-07, FDR  = 1.2e-04 and 2.4e-04, respectively). A third SNP, rs4869 (C10orf116), was additionally identified as significant in the exome sequencing data; it is in near-perfect LD with rs4934282. The associations with survival remained significant when somatic alterations.

Conclusions

Discovery analysis of TCGA data reveals germline genetic variations that may play a role in ovarian cancer survival even among late-stage cases. The significant loci are located near genes previously reported as having a possible relationship to platinum and taxol response. Because the variant alleles at the significant loci are common (frequencies for rs4934282 A/C alleles = 0.54/0.46, respectively; rs1857623 A/G alleles = 0.55/0.45, respectively) and germline variants can be assayed noninvasively, our findings provide potential targets for further exploration as prognostic biomarkers and individualized therapies.