Clusterin/Apo J protein expression in plasma samples of an elderly Sardinian population

Clusterin (CLU) is a glycoprotein with a nearly ubiquitous tissue distribution that has been reported to be implicated in several physiological processes as well as in many pathological conditions including ageing, diabetes, atherosclerosis, degenerative diseases and tumorigenesis. In this work we studied the changes in the CLU protein expression in plasma samples of a Sardinian population divided by age into four groups. We applied a proteomic approach using 2D-PAGE-MS analyses, western immunoblotting and ELISA to perform comparisons between the four groups. The typical train of spots of the Clusterin protein in a 2D plasma map was examined and according to statistical analyses five spots were detected as being differentially expressed within the four groups. Regarding total Clusterin the results agree with the data shown by literature but only values up to 90 years old have been reported for Clusterin protein expression. This work extends to older people showing that after 90 a decrease in plasma Clusterin levels seems to occur especially in centenarians. Considering that Clusterin is a sensitive biosensor of oxidative stress it could be in accordance with the fact that centenarians, considered as a model of successful ageing, are characterized by low levels of ROS (radical oxygen species)

Book of abstracts: Scientific Opening of The Microsoft Reasearch Centre for Computational and Systems Biology, Trento, Italy, April 3-5, 2006

Abstracts of the talks of the Scientific Opening of the Microsoft Research - University of Trento Centre for Computational and Systems Biology held in Trento on April 3-5, 200

Plasma clusterin and lipid profile: a link with aging and cardiovascular diseases in a population with a consistent number of centenarians

The role of Clusterin in attenuation of inflammation and reverse cholesterol transfer makes this molecule a potential candidate as a marker for cancer, cardiovascular disease, diabetes mellitus, and metabolic syndrome. In elderly subjects cardiovascular diseases represent the primary cause of death and different clinical studies have shown a positive correlation of these diseases with changes in the lipid pattern. This work aimed at evaluating the relationship between circulating clusterin and the biochemical parameters that characterize the lipid profile of a Sardinian population divided into five age groups including centenarians; the high frequency in Sardinia of these long-lived individuals gave us the opportunity to extend the range of the age groups to be analyzed to older ages and to better evaluate the changes in the lipid balance during ageing and its relationship with clusterin concentration in plasma. Our results showed that Clusterin concentration values of the youngest group were more similar with the centenarian’s group compared to the other age groups, and a positive correlation arises with LDL. Furthermore given the high prevalence of cardiovascular diseases in the population examined and the association of Clusterin with these pathologies we evaluated Clusterin concentration variation in two groups with or without cardiovascular diseases. In presence of cardiovascular disease, Clusterin is significantly related to the most atherogenic components of lipid profile (total cholesterol and LDL), especially in women, suggesting its potential role in modulating cardiovascular metabolic risk factors

Cholesterol lowering treatment restores blood global DNA methylation in chronic kidney disease (CKD) patients

This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (June 2017) in accordance with the publisher’s archiving policyBackground and aims Chronic kidney disease (CKD) is characterized by increased oxidative stress (OS). In consideration of the well-known link between OS and DNA methylation we assessed DNA methylcytosine (mCyt) concentrations in CKD patients at baseline and during cholesterol lowering treatment. Methods and results DNA methylation and OS indices (malonyldialdehyde, MDA; allantoin/uric acid ratio, All/UA) were measured in 30 CKD patients randomized to three cholesterol lowering regimens for 12 months (simvastatin 40 mg/day, ezetimibe/simvastatin 10/20 mg/day, or ezetimibe/simvastatin 10/40 mg/day) and 30 age- and sex-matched healthy controls. DNA methylation was significantly lower in CKD patients vs. controls (4.06 ± 0.20% vs. 4.27 ± 0.17% mCyt, p = 0.0001). Treatment significantly increased mCyt DNA concentrations in all patients (4.06 ± 0.04% at baseline; 4.12 ± 0.03% at 4 months; 4.17 ± 0.03% at 8 months; and 4.20 ± 0.02% at 12 months, p = 0.0001 for trend). A trend for a greater effect on DNA methylation was observed with combined treatment ezetimibe/simvastatin 10/40 mg/day (+5.2% after one year treatment). The treatment-associated mCyt increase was significantly correlated with the concomitant reduction in MDA concentrations and All/AU ratios. Conclusion Our results demonstrate that CKD patients have a lower degree of DNA methylation and that cholesterol lowering treatment restores mCyt DNA concentrations to levels similar to healthy controls. The treatment-associated increase in DNA methylation is correlated with a concomitant reduction in OS markers. The study was registered at clinicaltrials.gov (NCT00861731)

Modeling and parameter estimation of the SOS response network in E.coli

The SOS response is an inducible DNA repair system that allows bacteria to survive in presence of an increased level of DNA damage. More than 40 genes are induced in response to DNA damage as part of the SOS regulon in Escherichia coli. Two main proteins play a key role in the regulation of this response: a repressor LexA that prevents the expression of these genes and an inducer RecA that induces the LexA cleavage reaction and the subsequent expression of the response genes. Most of these response genes are responsible for error-free DNA-damage repair and for the regulation of cell division. In this thesis we have investigated a network of nine genes including the principal mediators of the SOS response: lexA, recA, ssB, recF, dinI and umuDC and three sigma factor genes: rpoD, rpoH and rpoS

Inferring gene networks: dream or nightmare?: Part 1: challenges 1 and 3

Inferring gene networks is a daunting task. We here describe several algorithms we used in the Dialogue for Reverse Engineering Assessments and Methods (DREAM2) Reverse Engineering Competition 2007: an algorithm based on first-order partial correlation for discovering BCL6 targets in Challenge 1 and an algorithm using nonlinear optimization with winning performance in Challenge 3. After the gold standards for the challenges were released, the performance of alternative variants of the algorithms could be evaluated. The DREAM competition taught us some strong lessons. Amazingly, simpler methods performed in general better than more advanced, theoretically motivated approaches. Also, the challenges strongly showed that inferring gene networks requires controlled experimentation using a well-defined experimental design. Analyzing data obtained through merging many unrelated datasets indeed resulted in weak performances of all algorithms, while algorithms that explicitly took the experimental design into account performed best

Effects of Ramipril and Telmisartan on Plasma Concentrations of Low Molecular Weight and Protein Thiols and Carotid Intima Media Thickness in Patients with Chronic Kidney Disease

Hypertension, a common feature in chronic kidney disease (CKD), is an independent risk factor for CKD progression and cardiovascular disease. Although inhibitors of the renin-angiotensin system (RAS) exert salutary effects on blood pressure control and proteinuria in CKD patients, their activity towards traditional and novel oxidative markers is largely unknown. We studied the effects of 6-month treatment with telmisartan versus a combination of telmisartan and ramipril on plasma concentrations of low molecular mass (LMW, including homocysteine and cysteine) and protein thiols (PSH) plasma concentration and their relationships with carotid intima media thickness (IMT), in 24 hypertensive CKD patients (age 60±12 years, 8 females and 16 males). Pretreatment PSH concentrations were independently associated with IMT (r=-0.42, p=0.039). Neither treatment affected plasma LMW thiols, in both reduced and total form. By contrast, both treatments increased PSH plasma concentrations and reduced IMT, although significant differences were only observed in the combined treatment group. Our results suggest that the beneficial effects of combined RAS inhibitor treatment on IMT in hypertensive CKD patients may be mediated by a reduction of oxidative stress markers, particularly PSH

miRNA Stability in Frozen Plasma Samples

MicroRNAs (miRNAs) represent a family of small non-coding ribonucleic acids that post-transcriptionally inhibits the expression of their target messenger RNAs (mRNAs), thereby acting as general gene repressors. In this study we examined the relative quantity and stability of miRNA subjected to a long period of freezing; we compared the stability of eight miRNAs in the plasma of five human healthy controls before freezing and after six and 12 months of storage at −80 °C. In addition, we examined the plasma frozen for 14 years and the amount of miRNA still available. Using a Life Technologies protocol to amplify and quantify plasma miRNAs from EDTA (Ethylene Diamine Tetraacetic Acid)-treated blood, we analyzed the stability of eight miRNAs, (miR-125b-5p, miR-425-5p, miR-200b-5p, miR-200c-3p, miR-579-3p, miR-212-3p, miR-126-3p, and miR-21-5p). The miRNAs analyzed showed a high stability and long frozen half-life

Lipid parameters’ values in the five age groups.

<p>Boxplots represent the Lipid parameters analysed in the five age groups, total cholesterol, LDL (low density lipoprotein), HDL (high density lipoprotein) and Triglycerides. Circles represent outliers and asterix extreme outliers.</p