Insights into lipid-protein interactions from computer simulations.

Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.

Clinical and laboratory markers of autosomal dominant polycystic kidney disease (ADPKD) progression: an overview.

Autosomal dominant polycystic kidney (ADPKD) is the most common inherited renal cystic disease and it occurs in all races, the reported prevalence is between 1:400 and 1:1000. It is characterized by development of cysts in both kidneys and progressive renal function loss. Among most Autosomal Dominant Polycystic Kidney patients, renal function remains intact until the fourth decade of life. It is very important to identify early markers of disease progression to recognize patients with a worse prognosis. The aim of this study is to review the clinical and laboratory markers of ADPKD progression. The early clinical parameters evaluated seem to be directly correlated with the volume of the cysts that determine the kidney volume. From a clinical point of view, total kidney volume (TKV) appears to be the best marker of early ADPKD progression. This review evaluated several ADPKD progression markers comparing the early consolidated clinical and the new promising laboratory indicators. From a laboratory point of view, copeptin has a potential role between the serum biomarkers of ADPKD progression. However, further studies are necessary to validate the potential predictive value of its serum level and to adopt it for routine use. The combination of biomarkers could probably predict ADPKD progression with more accuracy than the use of a single biomarker.

Purity and stability of online-prepared hemodiafiltration fluid after storage.

BACKGROUND/AIMS: Previous studies have suggested that online hemodiafiltration (OL-HDF) fluid can be used as dialysate for continuous renal replacement therapies, and thus HDF costs can be reduced. The aims of this study were to determine the purity of OL-HDF fluid and to verify the stability of the electrolyte composition and acid-base balance during its storage. METHODS: OL-HDF fluid was collected in 70 individual bags and stored for up to 7 days. The following tests were performed daily in 10 bags: natural visible precipitation (macrocrystallization), sample collection for chemical analysis and fluid culture, limulus amebocyte lysate endotoxin test, standard culture of NALGENE® filters after passing of the fluid, and molecular analysis of bacterial DNA. RESULTS: The values of pH and pCO(2) showed a significant change starting at 24 h (p < 0.001); after 72 h, their values were beyond the measurable range. Coefficient of variation for pCO(2) was as high as 25.7%. Electrolyte composition (Na(+), K(+), Cl(-), Ca(2+) and glucose) showed a statistically significant difference over time (p < 0.05); however, their coefficients of variation were low (1.7, 1.4, 0.6, 2.3 and 0.9%, respectively), which might not be considered clinically significant. Negative results were obtained at all points by fluid and filter cultures, endotoxin test and molecular analysis. No macrocrystallization was observed at any time point. CONCLUSIONS: We demonstrate the microbiological purity of OL-HDF fluid stored for up to 7 days. The electrolyte composition was stable, except for a relevant change in pCO(2) and consequently in pH (first noted at 24 h), emphasizing the need to reassess the acid-base balance in multilayer plastic bags in future studies.

Clinical pattern of adult polycystic kidney disease in a northeastern region of Italy.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic renal disorder, with a prevalence of 1 : 500 to 1 : 1,000. ADPKD is genetically heterogeneous: the genes involved are PKD1 and PKD2. ADPKD occurs worldwide and in all ethnic groups and is an important cause of CKD Stage 5. Prevalence of ADPKD on renal replacement therapy (RRT) in Italy has been reported to be 8.2%. In the dialysis population of Vicenza, a province in Northeastern Italy, it accounts for 13.4%. The study aims to investigate reasons for the high prevalence of ADPKD in our region and to describe the clinical profile and genetics of these patients. METHODS: Since April 2007, ADPKD patients have been enrolled. Patients from families not native to Vicenza have been excluded. The diagnosis of ADPKD is defined by ultrasound criteria. Complete clinical details have been recorded, including family history. We have used linkage analysis to identify the gene involved in each family. RESULTS: We describe the first 100 patients recruited from a total of 42 families. 29 patients were in ESRD at the time of enrollment. Renal stones and hepatic cysts were present in 24% and 40%, respectively. The majority of the ADPKD patients (61%) were diagnosed either incidentally or by screening. Positive family history was recorded in 86 patients. The involved gene was PKD1 in 83.7% and PKD2 in 16.3% of the studied patients. PKD2 patients presented the common haplotype. CONCLUSIONS: It is the first epidemiological study from Northeastern Italy reporting clinical profile and genetic analysis of ADPKD patients. The clinical profile of the patients is similar to previous reports, but there is a high prevalence of ADPKD in our region. The presence of a common haplotype is in accordance with our hypothesis of a founder effect in our province, suggesting that a strong lineage-specific gene is present. If the sequence analysis confirms the same mutation, this might suggest a common ancestral origin and a segregation of a specific mutation.

Effect of vitamin E-coated dialysis membranes on anemia in patients with chronic kidney disease: an Italian multicenter study.

BACKGROUND: Increased oxidant stress is increasingly recognized as a crucial factor in anemia in patients with chronic kidney disease. Vitamin E-coated membranes (VECMs) consist of a multilayer membrane with liposoluble vitamin E on the blood surface allowing direct free radical scavenging at the membrane site, which is of potential clinical benefit. Our objective was to examine the effect of VECMs on anemia in chronic hemodialysis (HD). METHODS: We enrolled 172 stable chronic HD patients (94 men, 78 women, age 65.4 +/- 13.4 years) in an open-label multicenter study. They were shifted from their previous dialyzer to VECM for 1 year. Hemoglobin (Hb) levels and recombinant human erythropoietin (rHuEpo) dosage were analyzed after 4, 8, and 12 months on the VECM and compared with baseline values using paired tests. RESULTS: Hb significantly increased from 10.9 +/- 1.2 g/dL at baseline to 11.7 +/- 1.2 g/dL after 12 months (p<0.001) on VECMs. Conversely, the rHuEpo dosage decreased from 7,762 +/- 5,865 IU/week at baseline to 6,390 +/- 5,679 IU/week after 12 months (p<0.001). The proportion of patients who were at target Hb levels (European Best Practice Guidelines) increased from 49.4% at baseline to 80% after 12 months (p<0.001). CONCLUSIONS: Dialysis with VECM in stable chronic HD patients was associated with significantly improved Hb levels and lower rHuEpo requirements. These results suggest that the antioxidant properties of VECMs may impact favorably on anemia management in chronic HD patients. Possible mechanisms include enhanced membrane biocompatibility, reduced oxidative stress and inflammation with VECMs, resulting in improved red blood cell survival and/or rHuEpo responsiveness. This therapy may potentially contribute to more effective anemia management in hemodialysis patients, and merits further rigorous study.

Inflammation and subclinical infection in chronic kidney disease: a molecular approach.

Inflammation and infection seem to be important causes of morbidity and mortality in chronic kidney disease (CKD) patients; subclinical infections have been proposed as an important cause of inflammatory syndrome, but to date this hypothesis remains speculative. We developed a method for the molecular detection of the presence of bacterial DNA in a population of CKD patients in order to correlate the molecular data with the degree and level of inflammation and to evaluate its usefulness in the diagnosis of subclinical infection. The study was divided into two phases: (1) a population of 81 CKD patients was screened for the prevalence and level of inflammation and the presence of possible infection, and (2) a subgroup of 38 patients, without evident clinical causes of inflammation, underwent complete molecular evaluation for subclinical infection using bacterial DNA primers for sequencing. Additionally, complete analysis was carried out in the blood and dialysate compartments of the hemodialyzers used. The general population showed a certain degree of subclinical inflammation and no difference was found between patients with and without evident causes of inflammation. Hemoculture-negative patients were positive for the presence of bacterial DNA when molecular methods were used. We found a correlation trend between the presence of bacterial DNA and the increase in hs-CRP, IL-6 and oxidative stress (advanced oxidation protein product) levels and a reduction in the mean fluorescence intensity for HLA-DR. Hemodialyzer membranes seem to have properties that stick to bacteria/bacterial DNA and work as concentrators. In fact, patients with negative bacterial DNA in the circulating blood displayed positivity in the blood compartment of the dialyzer. The dialysate was negative for bacterial DNA but the dialysate compartment of the hemodialyzers used was positive in a high percentage. Moreover our data suggest that bacterial DNA can traverse hemodialysis membranes. Molecular methods have been found to be far more sensitive than standard methods in detecting subclinical infection. The presence of bacterial DNA seems to influence the variation in some parameters of inflammation and immunity. Apart from the limitations and pitfalls, the molecular method could be useful to screen for subclinical infection and diagnose subclinical sepsis when the hemoculture is negative. However, the identification of the microorganism implicated must be done with species-specific primers.

Regularized neural networks: some convergence rate results.

In a recent paper, Poggio and Girosi (1990) proposed a class of neural networks obtained from the theory of regularization. Regularized networks are capable of approximating arbitrarily well any continuous function on a compactum. In this paper we consider in detail the learning problem for the one-dimensional case. We show that in the case of output data observed with noise, regularized networks are capable of learning and approximating (on compacta) elements of certain classes of Sobolev spaces, known as reproducing kernel Hilbert spaces (RKHS), at a nonparametric rate that optimally exploits the smoothness properties of the unknown mapping. In particular we show that the total squared error, given by the sum of the squared bias and the variance, will approach zero at a rate of n(-2m)/(2m+1), where m denotes the order of differentiability of the true unknown function. On the other hand, if the unknown mapping is a continuous function but does not belong to an RKHS, then there still exists a unique regularized solution, but this is no longer guaranteed to converge in mean square to a well-defined limit. Further, even if such a solution converges, the total squared error is bounded away from zero for all n sufficiently large.