Positively charged surfaces increase the flexibility of DNA

Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how ions change the flexibility of DNA in solution, but when considering macromolecules such as chromatin in which the DNA contacts the nucleosome core each turn of the double helix, it may be more appropriate to assess the flexibility of DNA on charged surfaces. Mica coated with positively charged molecules is a convenient substrate upon which the flexibility of DNA may be directly measured with a scanning force microscope. In the experiments described below, the flexibility of DNA increased as much as fivefold depending on the concentration and type of polyamine used to coat mica. Using theory that relates charge neutralization to flexibility, we predict that phosphate repulsions were attenuated by approximately 50% in the most flexible DNA observed. This simple method is an important tool for investigating the physiochemical causes and molecular biological effects of DNA flexibility, which affects DNA biochemistry ranging from chromatin stability to viral encapsulation.     

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina''s MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.     

Electrical stimulation of glossopharyngeal nerve and oesophageal EMG response in the pigeon

The effects of the efferent glossopharyngeal nerve stimulation, on EMG activity of the pigeon cervical oesophagus, were studied. In control animals, stimulation caused a biphasic response characterized by an intra-stimulus excitatory component followed by a post-stimulus inhibitory one. The EMG response to glossopharyngeal stimulation appeared simultaneously throughout the cervical oesophagus. A bell-shaped mechanical wave was detected relating to the electrical excitatory component. Atropine administration antagonized the excitatory component, while the inhibitory one persisted. It occurs intra-stimulus, and its duration is increased, compared to control ones. A reduction in the oesophageal resting pressure was observed relating to the electrical inhibitory component. Hexamethonium caused complete disappearance of any EMG response to glossopharyngeal stimulation, as well as suppression of mechanical responses. The comparison between the EMG responses to swallow and to efferent glossopharyngeal stimulation suggests that in pigeon cervical oesophagus: primary peristalsis is central in origin; a dual system of glossopharyngeal fibres, excitatory and inhibitory, carries the central control for oesophageal motility; these excitatory and inhibitory fibres supply the oesophageal muscle via intramural neurons; the synaptic arrangement of the inhibitory pathway is more complex than the excitatory one.     

Blood rheology of Weddell seals and bowhead whales

Red blood cell (RBC) aggregation and blood viscosity are important determinants of in vivo blood flow dynamics and, in marine mammals, these parameters may impact diving physiology by altering blood oxygen delivery during the diving response. Weddell seals are superb divers and exhibit age-related patterns in blood oxygen chemistry and diving ability. By contrast, bowhead whales are not long duration divers, and little is known of their blood properties relative to diving. The present study was designed to compare rheological characteristics of blood from Weddell seal pups, Weddell seal adults, and from adult bowhead whales: blood viscosity and RBC aggregation in plasma and in polymer solutions (i.e., RBC "aggregability") were measured. Salient findings included: (1) significant 4- to 8-fold greater aggregation in blood from adult seals compared with pups and human subjects; (2) 2-to 8-fold greater aggregation in bowhead whale blood compared with human blood; (3) compared to human red cells, enhanced RBC aggregability of RBC from adult seals and whales as determined by their greater aggregation in polymer solutions; (4) increasing RBC aggregation and aggregability of seal pup blood over a seven day period following birth; (5) significantly greater blood viscosity for adult seals compared with pups at both native and standardized hematocrits. These results indicate that, for both species, hemorheological parameters differ markedly from those of humans, and suggest progressive changes with seal age; the physiological implications of these differences have yet to be fully defined.     

Solid phase subtractive cloning in differentially expressed genes identification

We developed an array-based subtractive hybridization system for one-step high-throughput subtraction. We printed subtractor RNA up to 10.000 times obtaining an excellent contact surface using a little amount of RNA. During hybridization cDNA, common to subtractor and target samples, remains attached to slide immobilized RNA, leaving free in solution target specific cDNA which after retrieval is cloned.     

The activation of liver X receptors inhibits toll‐like receptor‐9‐induced foam cell formation

Toll‐like receptors (TLRs) are related to foam cell formation (FCF), key event in the establishment/progression of atherosclerosis. The activation of TLR2 and TLR4 can increase FCF. The aim of this study was to evaluate the role of TLR9 in FCF. Murine macrophages were treated with CpG‐ODN, TLR9 agonist, and oxidized particles of LDL (Paz‐PC) and FCF was analyzed by means of Oil Red O staining. The administration of CpG‐ODN plus Paz‐PC onto macrophages increased the amount of lipid droplets, correlated to increased levels of tumor necrosis factor (TNF)‐α, IFNβ, and IP‐10. The underlying mechanism by which TLR9 ligation influenced Paz‐PC in the FCF was NF‐κB‐ and IRF7‐dependent, as observed by higher levels of phosphorylated IκBα, increased nuclear translocation of the p65 subunit, lower levels of the total IKKα protein and higher release of interferon‐dependent cytokines, such as IP‐10. Liver X receptors (LXRs) regulate lipid cellular transport and negatively modulate TLR‐dependent signaling pathways. Indeed, the addition of GW3965, synthetic LXRs agonist, significantly reduced FCF after CpG‐ODN plus Paz‐PC stimulation. In this condition, we observed decreased levels of the nuclear translocation of the p65 subunit, related to the higher presence of LXRα into the nucleus. TNF‐α, IP‐10, and IFNβ levels were reduced by the administration of GW3965 following CpG‐ODN and Paz‐PC treatment. In conclusion, the activation of TLR9 facilitates the formation of foam cells in an NF‐κB‐ and IRF7‐dependent manner, countered by the activation of LXRs. This study further support LXRs as potential anti‐atherosclerotic target. J. Cell. Physiol. 223: 158–167, 2010. © 2009 Wiley‐Liss, Inc.     

Study of the ecology of fresh sausages and characterization of populations of lactic acid bacteria by molecular methods

In this study, a polyphasic approach was used to study the ecology of fresh sausages and to characterize populations of lactic acid bacteria (LAB). The microbial profile of fresh sausages was monitored from the production day to the 10th day of storage at 4 degrees C. Samples were collected on days 0, 3, 6, and 10, and culture-dependent and -independent methods of detection and identification were applied. Traditional plating and isolation of LAB strains, which were subsequently identified by molecular methods, and the application of PCR-denaturing gradient gel electrophoresis (DGGE) to DNA and RNA extracted directly from the fresh sausage samples allowed the study in detail of the changes in the bacterial and yeast populations during storage. Brochothrix thermosphacta and Lactobacillus sakei were the main populations present. In particular, B. thermosphacta was present throughout the process, as determined by both DNA and RNA analysis. Other bacterial species, mainly Staphylococcus xylosus, Leuconostoc mesenteroides, and L. curvatus, were detected by DGGE. Moreover, an uncultured bacterium and an uncultured Staphylococcus sp. were present, too. LAB strains isolated at day 0 were identified as Lactococcus lactis subsp. lactis, L. casei, and Enterococcus casseliflavus, and on day 3 a strain of Leuconostoc mesenteroides was identified. The remaining strains isolated belonged to L. sakei. Concerning the yeast ecology, only Debaryomyces hansenii was established in the fresh sausages. Capronia mansonii was initially present, but it was not detected after the first 3 days. At last, L. sakei isolates were characterized by randomly amplified polymorphic DNA PCR and repetitive DNA element PCR. The results obtained underlined how different populations took over at different steps of the process. This is believed to be the result of the selection of the particular population, possibly due to the low storage temperature employed.     

Chlamydia pneumoniae-induced foam cell formation requires MyD88-dependent and -independent signaling and is reciprocally modulated by liver X receptor activation

Chlamydia pneumoniae is detected by macrophages and other APCs via TLRs and can exacerbate developing atherosclerotic lesions, but how that occurs is not known. Liver X receptors (LXRs) centrally control reverse cholesterol transport, but also negatively modulate TLR-mediated inflammatory pathways. We isolated peritoneal macrophages from wild-type, TLR2, TLR3, TLR4, TLR2/4, MyD88, TRIF, MyD88/TRIF, and IFN regulatory factor 3 (IRF3) KO mice, treated them with live or UV-killed C. pneumoniae in the presence or absence of oxidized LDL, then measured foam cell formation. In some experiments, the synthetic LXR agonist GW3965 was added to macrophages infected with C. pneumoniae in the presence of oxidized LDL. Both live and UV-killed C. pneumoniae induced IRF3 activation and promoted foam cell formation in wild-type macrophages, whereas the genetic absence of TLR2, TLR4, MyD88, TRIF, or IRF3, but not TLR3, significantly reduced foam cell formation. C. pneumoniae-induced foam cell formation was significantly reduced by the LXR agonist GW3965, which in turn inhibited C. pneumoniae-induced IRF3 activation, suggesting a bidirectional cross-talk. We conclude that C. pneumoniae facilitates foam cell formation via activation of both MyD88-dependent and MyD88-independent (i.e., TRIF-dependent and IRF3-dependent) pathways downstream of TLR2 and TLR4 signaling and that TLR3 is not involved in this process. This mechanism could at least partly explain why infection with C. pneumoniae accelerates the development of atherosclerotic plaque and lends support to the proposal that LXR agonists might prove clinically useful in suppressing atherogenesis.     

Stem cells and growth factor delivery systems for cardiovascular disease

Coronary (CAD) and peripheral (PAD) artery diseases are major causes of morbidity and mortality, and millions of CAD and PAD patients are treated by various medications, bypass surgery or angioplasty around the world. Such patients might benefit from novel stem cells and tissue engineering strategies aimed at accelerating natural processes of postnatal collateral vessel formation and repairing damaged tissues. By combining three fundamental “tools”, namely stem cells, biomaterials and growth factors (GFs), such strategies may enhance the efficacy of cell therapy in several ways: (a) by supplying exogenous stem cells or GFs that stimulate resident cardiac stem cell (CSC) migration, engraftment and commitment to cardiomyocytes, and that induce and modulate arterial response to ischemia; (b) by supporting the maintenance of GFs and transplanted stem cells in the damaged tissues through the use of biocompatible and biodegradable polymers for a period of time sufficient to allow histological and anatomical restoration of the damaged tissue. This review will discuss the potential of combining stem cells and new delivery systems for growth factors, such as vehicle-based delivery strategies or cell-based gene therapy, to facilitate regeneration of ischemic tissues. These approaches would promote the ability of resident CSCs or of exogenous multipotent stem cells such as adipose tissue-derived mesenchymal stem cells (AT-MSCs) to induce the healing of damaged tissue, by recruiting and directing these cells into the damage area and by improving angiogenesis and reperfusion of ischemic tissues.