PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes our repository freely accessed and easily edited by any scientists. To this purpose, we encourage plant biologist experts to join our annotation effort and share their knowledge on resistance-gene biology with the rest of the scientific community.

Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations.

BACKGROUND: Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits. RESULTS: Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars. CONCLUSIONS: The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.

miR-338-3p is over-expressed in blood, CFS, serum and spinal cord from sporadic amyotrophic lateral sclerosis patients.

Amyotrophic lateral sclerosis (ALS) is a progressive and seriously disabling adult-onset neurological disease. Ninety percent of ALS patients are sporadic cases (sALS) with no clear genetic linkage. Accumulating evidence indicates that various microRNAs (miRNAs), expressed in a spatially and temporally controlled manner in the brain, play a key role in neuronal development. In addition, microRNA dysregulation contributes to some mental disorders and neurodegeneration diseases. In our research, the expression of one selected miRNA, miR-338-3p, which previously we have found over-expressed in blood leukocytes, was studied in several different tissues from sALS patients. For the first time, we detected a specific microRNA disease-related upregulation, miR-338-3p, in blood leukocytes as well in cerebrospinal fluid, serum, and spinal cord from sALS patients. Besides, staining of in situ hybridization showed that the signals of miR-338-3p were localized in the grey matter of spinal cord tissues from sALS autopsied patients. We propose that miRNA profiles found in tissue samples from sALS patients can be relevant to understand sALS pathogenesis and lead to set up effective biomarkers for sALS early diagnosis.

Telomerase expression in amyotrophic lateral sclerosis (ALS) patients.

Telomerase and telomeric complex have been linked to a variety of disease states related to neurological dysfunction. In amyotrophic lateral sclerosis (ALS) patients, telomerase activity, as human telomerase reverse transcriptase (hTERT) expression, has not been characterized yet. Here, for the first time, we characterized telomerase and related pathway in blood sample and spinal cord from ALS patients compared with healthy controls. We found that hTERT expression level was significantly lower in ALS patients and was correlated either to p53 mRNA expression or p21 expression, pointing out the hypothesis that telomerase inhibition could be a pathogenetic contributor to neurodegeneration in ALS. As a consequence of the reduced telomerase activity, we identified shorter telomeres in leukocytes from sporadic ALS patients compared with healthy control group.

Comparative transcriptional analysis reveals differential gene expression between Sand Daffodil tissues.

Sand Daffodil (Pancratium maritimum) is a world-wide endangered Amayllidaceae species and represents an important anti-cancer medicinal resource due to alkaloids production. Despite its increasing pharmaceutical importance, there are not molecular resources that can be utilized toward improving genetic traits. In our research, the suppression subtractive hybridization (SSH) method conducted to generate large-scale expressed sequence tags (EST), was designed to identify gene candidates related to the morphological and physiological differences between the two tissues, leaves and bulbs, since lycorine, the main anti-cancer compound, is there synthesized. We focused on identification of transcripts in different tissues from Sand Daffodil using PCR-based suppression SSH to identify genes involved in global pathway control. Sequencing of 2,000 differentially screened clones from the SSH libraries resulted in 136 unigenes. Functional annotation and gene ontology analysis of up-regulated EST libraries showed several known biosynthetic genes and novel transcripts that may be involved in signaling, cellular transport, or metabolism. Real time RT-PCR analysis of a set of 8 candidate genes further confirmed the differential gene expression.

Association between exposure to dioxin-like polychlorinated biphenyls and miR-191 expression in human peripheral blood mononuclear cells.

Accumulating evidence shows an association between deregulation of miRNAs and exposure to environmental chemicals; miRNAs play a unique regulatory role in gene expression. Among environmental pollutants, dioxins are a family of compounds that are known to have multiple hazardous effects. Also, in utero exposure of the fetus to dioxins has been shown to cause impaired psychomotor development, decreased immune function and skin disease. miR-191 is a microRNA that has been found to be up-regulated by dioxin in hepatocellular carcinoma cells in vitro. Our study provides the first molecular evidence in vivo of a positive relationship between levels of polychlorinated biphenyls (PCBs) and miR-191 expression in human peripheral blood mononuclear cells. miR-191 expression was significantly correlated with blood concentrations of total PCB and, in particular, of 3,3',4,4',5,5'-hexachlorobiphenyl (PCB 169, a coplanar congener). Blood concentrations of PCB 169 correlated significantly with miR-191 expression in pregnant women living in a PCB-polluted area, who underwent therapeutic abortion due to fetal malformations. These data suggest that miRNAs could be potential biomarkers to clarify the mechanisms of environmental disease.

Takotsubo cardiomyopathy: do the genetics matter?

Takotsubo cardiomyopathy (TTC) is an enigmatic disease with a multifactorial and still unresolved pathogenesis. Recent experimental and clinical observation has suggested a role for genetics in the pathogenesis of TTC. Ethnic as well as seasonal variation in the prevalence of TTC is well described, but it is only recently that familial cases of TTC have been reported. In recent years technological advances in exome capture and DNA sequencing have offered clinicians a new opportunity to discover genetics-related disease. This article explores the role of genetic mechanisms that might explain or modulate the pathogenesis of TTC.

Cardiotrophin-1 and TNF-alpha circulating levels at rest and during cardiopulmonary exercise test in athletes and healthy individuals.

BACKGROUND: There is a growing body of evidence that physical training exerts its potential benefits on the individual health status by modulating the immune system and the whole body metabolism. A better knowledge of the physiologic immune response to exercise may help to understand the benefits of physical exercise in healthy individuals and elite athletes. AIMS: This study aims to analyse cardiotrophin-1 (CT-1) and Tumor Necrosis Factor-alpha (TNF-alpha) plasma levels at rest and during exercise in elite athletes and healthy controls. METHODS: We studied 20 triathletes (TA) and 20 matched controls (CG). Chambers dimensions, left ventricular mass and left ventricular mass index were analysed by echocardiography. VO2 peak and VE/VCO2 were calculated by metabolic stress test. Blood samples were collected before the exercise session, at the exercise peak, and after the end of exercise. ELISA assays were used to measure CT-1 and TNF-alpha plasma levels. RESULTS: Among TA and CG, no significant differences were found for CT-1 (0.25+/-0.14 vs 0.20+/-0.14 fm/l; p=0.29) and TNF-alpha (10.8+/-2.7 vs 9.7+/-4.0 pm/l; p=0.29) basal levels. In the TA, plasma levels of CT-1 were significantly different at rest and during exercise (basal 0.25+/-0.13 pm/l; peak 1.07+/-1.5 pm/l; post-exercise 0.67+/-0.77 pm/l; p=0.04). Conversely, no significant differences were found between basal, peak and post-exercise plasma values of TNF-alpha (basal 10.8+/-2.7 pm/l; peak 11.7+/-2.1 pm/l; post-exercise 11.4+/-2.5 pm/l; p=0.78) in TA. CONCLUSIONS: This study gives novel insights on the behavior of inflammatory cytokines during physical exercise in athletes and healthy individuals.

Assessment of DNA damage by RAPD in Paracentrotus lividus embryos exposed to amniotic fluid from residents living close to waste landfill sites.

The aim of this study was to assess the genotoxic effects of environmental chemicals on residents living near landfills. The study was based on samples of amniotic fluid from women living in the intensely polluted areas around the Campania region of Italy compared to a nonexposed control group. We evaluated the genetic effects that this amniotic fluids collected in contaminated sites had on Paracentrotus lividus embryos. DNA damage was detected through changes in RAPD (Random Amplified Polymorphism DNA) profiles. The absence of the amplified DNA fragments indicated deletions in Paracentrotus lividus DNA exposed to the contaminated amniotic fluids when compared to equal exposure to uncontaminated fluids. These results show the ability of RAPD-PCR to detect and isolate DNA sequences representing genetic alterations induced in P. lividus embryos. Using this method, we identified two candidate target regions for DNA alterations in the genome of P. lividus. Our research indicates that RAPD-PCR in P. lividus embryo DNA can provide a molecular approach for studying DNA damage from pollutants that can impact human health. To our knowledge, this is the first time that assessment of DNA damage in P. lividus embryos has been tested using the RAPD strategy after exposure to amniotic fluid from residents near waste landfill sites.

Microbial diversity of landslide soils assessed by RFLP and SSCP fingerprints.

Landslides are a significant component of natural disasters in most countries around the world. Understanding these destructive phenomena through the analysis of possible correlations between microbial communities and the alteration of the soil responsible for landslides is important in order to reduce their negative consequences. To address this issue, bacterial and fungal communities in soils triggering landslides in Termini-Nerano and Massa Lubrense-Nerano (Naples, Italy) were analysed by genetic profiling techniques. Fingerprints were generated by single-strand conformation polymorphisms (SSCP) and random amplified polymorphic DNA (RAPD). The microbial community in both soil types was enriched in species which could contribute to the degradation process occurring during landslides, forming biofilms and leading to the transformation or the formation of minerals. Indeed, some of the identified bacteria were found to favour the transformation of clay minerals. These findings suggest a possible relationship between bacterial and fungal community-colonising soils and the occurrence of landslides.

Skeletal muscle involvement in cardiomyopathies.

The link between heart and skeletal muscle disorders is based on similar molecular, anatomical and clinical features, which are shared by the 'primary' cardiomyopathies and 'primary' neuromuscular disorders. There are, however, some peculiarities that are typical of cardiac and skeletal muscle disorders. Skeletal muscle weakness presenting at any age may indicate a primary neuromuscular disorder (associated with creatine kinase elevation as in dystrophinopathies), a mitochondrial disease (particularly if encephalopathy, ocular myopathy, retinitis, neurosensorineural deafness, lactic acidosis are present), a storage disorder (progressive exercise intolerance, cognitive impairment and retinitis pigmentosa, as in Danon disease), or metabolic disorders (hypoglycaemia, metabolic acidosis, hyperammonaemia or other specific biochemical abnormalities). In such patients, skeletal muscle weakness usually precedes the cardiomyopathy and dominates the clinical picture. Nevertheless, skeletal involvement may be subtle, and the first clinical manifestation of a neuromuscular disorder may be the occurrence of heart failure, conduction disorders or ventricular arrhythmias due to cardiomyopathy. ECG and echocardiogram, and eventually, a more detailed cardiovascular evaluation may be required to identify early cardiac involvement. Paediatric and adult cardiologists should be proactive in screening for neuromuscular and related disorders to enable diagnosis in probands and evaluation of families with a focus on the identification of those at risk of cardiac arrhythmia and emboli who may require specific prophylactic treatments, for example, pacemaker, implantable cardioverter-defibrillator and anticoagulation.

Natriuretic peptides: molecular biology, pathophysiology and clinical implications for the cardiologist.

Natriuretic peptides (NPs) counter the effects of volume overload or adrenergic activation of the cardiovascular system. They are able to induce arterial vasodilatations, natriuresis and diuresis, and they reduce the activities of the renin-angiotensin-aldosterone system and the sympathetic nervous system. However, in addition to wall stress, other factors have been associated with elevated natriuretic peptide levels. Since 2000, because of their characteristics, NPs have become quantitative plasma biomarkers of heart failure. Nowadays, NPs play an important role not only in the diagnosis of heart failure, but also for a prognostic purpose and a guide to medical therapy. Finally, a new drug that modulates the NP system or recombinant analogs of NPs are now available in patients with heart failure.

Mitochondrial diseases and the heart: an overview of molecular basis, diagnosis, treatment and clinical course.

The mitochondrion is the main site of production of ATP that represents the source of energy for a large number of cellular processes. Mitochondrial diseases that result in a deficit in ATP production can affect almost every organ system with a large spectrum of clinical phenotypes. Cardiomyocytes are particularly vulnerable to limited ATP supply because of their large energy requirement. Abnormalities in the mitochondrial function are increasingly recognized in association with dilated and hypertrophic cardiomyopathy, cardiac conduction defects, endothelial dysfunction and coronary artery disease. Cardiologists should, therefore, be alerted to symptoms and signs suggestive of mitochondrial diseases and become familiar with the general issues related to multisystem disease management, genetic counseling and testing.

Analysis of endothelin-1 and endothelin-1 receptor A gene polymorphisms in patients with pulmonary arterial hypertension.

This study analyses the frequency and the potential role of two polymorphisms, the +134del/insA, located in the gene encoding for Endothelin-1 (EDN1), and the His323His in the gene encoding for Endothelin receptor type A (EDNRA) in a cohort of 98 consecutive patients with pulmonary arterial hypertension from two different Cardiology Units (Mid-South of Italy), and in 100 healthy Caucasian subjects randomly recruited from the same area. Cardiac anatomy and function were analysed by non invasive diagnostic imaging techniques (Echocardiography standard m-mode, 2D, colour-Doppler) and by invasive studies (cardiac catheterization). Molecular screening of the region of interest was performed by automated sequencing. At univariate analysis, patients with the His323His TT genotype show a lower cardiac index (2 ± 0.6 vs. 2.3 ± 0.6; p = 0.05) and a higher indexed pulmonary vascular resistance (18.8 ± 9.6 vs. 14.2 ± 6.9; p = 0.01) at cardiac catheterization. A logistic multivariate model shows idiopathic disease (p = 0.01; OR = 3.8; CI = 1.3-11) and indexed pulmonary vascular resistances (p = 0.01; OR = 1.1; CI = 1-1.2) as independent predictors of TT genotype. Our findings may suggest a potential link between specific genotypes in the EDNRA gene and susceptibility for PAH.