Cyclodextrins found in enzyme- and heat-processed starch-containing foods

Native and branched-type (glucosylated and maltosylated) cyclodextrins have been isolated and identified in different enzyme- and heat-processed starch-containing food products. Amylolytic enzyme-processed foods such as different beer samples, corn syrup of different dextrose equivalents, and thermally-processed food such as bread, contained minute amounts of different types of cyclodextrins. HPLC/MS Analyses of appropriately preconcentrated and purified food samples indicated the presence of parent beta- and gamma-cyclodextrins and all the three, alpha-, beta-, and gamma-branched cyclodextrins with different degrees of glycosylation. The data presented in this account are thought to be of practical importance in terms of both the analysis methods used for the cyclodextrins and the approval status of different cyclodextrin-containing food, cosmetic, and pharmaceutical products.     

The PHD finger, a nuclear protein-interaction domain

The PHD finger is a common structural motif found in all eukaryotic genomes. It is a Zn(2+)-binding domain and its closest structural relative is the RING domain. Many RING fingers bind to E2 ligases to mediate the ubiquitination of proteins. Whether PHD fingers share a common function is unclear. Notably, many if not all PHD fingers are found in nuclear proteins whose substrate tends to be chromatin. Some PHD fingers bind to specific nuclear protein partners, apparently through the same surface that is used by RING domains to bind their cognate E2 ligases. New evidence also suggests that some PHD fingers bind to nucleosomes, raising the possibility that chromatin might be a common nuclear ligand of PHD fingers.     

Comorbid Diseases Interact with Breast Cancer to Affect Mortality in the First Year after Diagnosis—A Danish Nationwide Matched Cohort Study

Background

Survival of breast cancer patients with comorbidity, compared to those without comorbidity, has been well characterized. The interaction between comorbid diseases and breast cancer, however, has not been well-studied.

Methods

From Danish nationwide medical registries, we identified all breast cancer patients between 45 and 85 years of age diagnosed from 1994 to 2008. Women without breast cancer were matched to the breast cancer patients on specific comorbid diseases included in the Charlson comorbidity Index (CCI). Interaction contrasts were calculated as a measure of synergistic effect on mortality between comorbidity and breast cancer.

Results

The study included 47,904 breast cancer patients and 237,938 matched comparison women. In the first year, the strongest interaction between comorbidity and breast cancer was observed in breast cancer patients with a CCI score of ≥4, which accounted for 29 deaths per 1000 person-years. Among individual comorbidities, dementia interacted strongly with breast cancer and accounted for 148 deaths per 1000 person-years within one year of follow-up. There was little interaction between comorbidity and breast cancer during one to five years of follow-up.

Conclusions

There was substantial interaction between comorbid diseases and breast cancer, affecting mortality. Successful treatment of the comorbid diseases or the breast cancer can delay mortality caused by this interaction in breast cancer patients.     

Integrated Analysis of Tumor Samples Sheds Light on Tumor Heterogeneity

The heterogeneity of tumor samples is a major challenge in the analysis of high-throughput profiling of tumor biopsies and cell lines. The measured aggregate signals of multigenerational progenies often represent an average of several tumor subclones with varying genomic aberrations and different gene expression levels. The goal of the present study was to integrate copy number analyses from SNP-arrays and karyotyping, gene expression profiling, and pathway analyses to detect heterogeneity, identify driver mutations, and explore possible mechanisms of tumor evolution. We showed the heterogeneity of the studied samples, characterized the global copy number alteration profiles, and identified genes whose copy number status and expression levels were aberrant. In particular, we identified a recurrent association between two BRAF^V600E and BRAF^V600K mutations and changes in DKK1 gene expression levels, which might indicate an association between the BRAF and WNT pathways. These findings show that the integrated approaches used in the present study can robustly address the challenging issue of tumor heterogeneity in high-throughput profiling.     

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.     

The reaction center is the sensitive target of the mercury(II) ion in intact cells of photosynthetic bacteria

The sensitivity of intact cells of purple photosynthetic bacterium Rhodobacter sphaeroides wild type to low level (<100 μM) of mercury (Hg2?) contamination was evaluated by absorption and fluorescence spectroscopies of the bacteriochlorophyll-protein complexes. All assays related to the function of the reaction center (RC) protein (induction of the bacteriochlorophyll fluorescence, delayed fluorescence and light-induced oxidation and reduction of the bacteriochlorophyll dimer and energization of the photosynthetic membrane) showed prompt and later effects of the mercury ions. The damage expressed by decrease of the magnitude and changes of rates of the electron transfer kinetics followed complex (spatial and temporal) pattern according to the different Hg2? sensitivities of the electron transport (donor/acceptor) sites including the reduced bound and free cytochrome c? and the primary reduced quinone. In contrast to the RC, the light harvesting system and the bc? complex demonstrated much higher resistance against the mercury pollution. The 850 and 875 nm components of the peripheral and core complexes were particularly insensitive to the mercury(II) ions. The concentration of the photoactive RCs and the connectivity of the photosynthetic units decreased upon mercury treatment. The degree of inhibition of the photosynthetic apparatus was always higher when the cells were kept in the light than in the dark indicating the importance of metabolism in active transport of the mercury ions from outside to the intracytoplasmic membrane. Any of the tests applied in this study can be used for detection of changes in photosynthetic bacteria at the early stages of the action of toxicants.     

Effects of orexin-monoaminergic interactions on oxytocin secretion in rat neurohypophyseal cell cultures

The effects of orexin-monoaminergic compound interactions on oxytocin release were studied in 14-day rat neurohypophyseal cell cultures prepared by an enzymatic dissociation technique. The oxytocin contents of the supernatants were determined by radioimmunoassay. Following the administration of orexin-A or orexin-B in increasing doses, significant changes were not observed in the oxytocin content of the supernatant media. The oxytocin level increased substantially in response to adrenaline, noradrenaline, serotonin, histamine, dopamine or K(+) treatment. Preincubation with orexin-A or orexin-B reduced the adrenaline-, histamine- or serotonin-induced oxytocin level increases, but the oxytocin concentrations of the supernatant media remained above the control level. There was no significant difference in decreasing effect between orexin-A and orexin-B. Neither orexin-A nor orexin-B induced changes in oxytocin release following monoaminergic compound treatment. The results indicate that the changes in oxytocin secretion induced by the monoaminergic system can be directly influenced by the orexin system. The effects of orexin on oxytocin release can be antagonized by an orexin-1 receptor-specific antagonist. It may be presumed that the orexins can play a role in the pathogenetic process of metabolic diseases (e.g. obesity) by reducing the effects of increased oxytocin release caused by monoaminergic compounds. The interactions between the monoaminergic and orexin systems regarding oxytocin secretion occur at both the hypothalamic and the neurohypophyseal levels.     

Major and trace elements in whole blood of phlebotomized patients with porphyria cutanea tarda

Porphyria cutanea tarda (PCT) is a disorder of hem biosynthesis resulting from a decreased activity of the uroporphyrinogen decarboxylase enzyme. Hem precursors are accumulated in the blood, liver and skin. Inherited and acquired factors also contribute to the pathogenesis of PCT. Hem precursors and porphyrins are excreted with urine and faeces. Whole blood of 8 PCT patients and 6 volunteers of Caucasian origin were analysed. In addition to routine laboratory measurements, 19 elements (Al, B, Ba, Ca, Cd, Co, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, S, V, Zn) were determined by means of inductively coupled plasma optical emission spectrometry (ICP-OES). Mg, P and S concentrations in whole blood were decreased significantly (p<0.05), whereas Ba was increased in PCT patients compared to controls. Metabolic alterations are reflected in the correlation of parameters. Positive correlations were found between the element pairs of Zn-Al, Zn-Mg, Zn-Mn, B-S, Fe-Mg, K-P, Mg-Mn for PCT patients, whereas in the control group Al-Mn, Ca-Cu, Ca-Na, Cu-Mg, Fe-K, Mg-Na, Zn-P showed positive correlations.