Cost-effectiveness of exome sequencing: an Italian pilot study on undiagnosed patients

Recent advances in genomic sequencing and their implementation in clinical practice are widely recognized as diagnostic milestones, and are influencing considerably medical decision making in term of patients’ management. The cost-effectiveness of genomic analysis as first-tier tests has been documented. However, only a few studies have assessed systematically the economic impact of a revised diagnostic trajectory based on exome sequencing in the health system for undiagnosed patients. We report on the assessment of diagnostic costs referred to a large cohort of patients enrolled in the Bambino Gesù Children’s Hospital’s “Undiagnosed Patients Program”, supporting the cost-effectiveness of exome sequencing in a universalistic health care service compared to the traditional multi-step diagnostic workup. Our data provide evidence that revision of health policy to promote genomic sequencing of patients with suspected Mendelian disorders would allow reallocation of resources for rare diseases from diagnostics to patient care. At a social level, diagnosis is crucial to receive the social “sick role” and establish an effective doctor-patient relationship. The application of genomic sequencing as first-tier diagnostic test does improve this process speeding up the diagnosis and management of undiagnosed patients.     

20-HETE Mediates Ozone-Induced,Neutrophil-Independent Airway Hyper-Responsiveness in Mice

Background

Ozone, a pollutant known to induce airway hyper-responsiveness (AHR), increases morbidity and mortality in patients with obstructive airway diseases and asthma. We postulate oxidized lipids mediate in vivo ozone-induced AHR in murine airways.

Methodology/Principal Findings

Male BALB/c mice were exposed to ozone (3 or 6 ppm) or filtered air (controls) for 2 h. Precision cut lung slices (PCLS; 250 µm thickness) containing an intrapulmonary airway (∼0.01 mm² lumen area) were prepared immediately after exposure or 16 h later. After 24 h, airways were contracted to carbachol (CCh). Log EC₅₀ and E_max values were then calculated by measuring the airway lumen area with respect to baseline. In parallel studies, dexamethasone (2.5 mg/kg), or 1-aminobenzotriazol (ABT) (50 mg/kg) were given intraperitoneal injection to naïve mice 18 h prior to ozone exposure. Indomethacin (10 mg/kg) was administered 2 h prior. Cell counts, cytokine levels and liquid chromatography-mass spectrometry (LC-MS) for lipid analysis were assessed in bronchoalveolar lavage (BAL) fluid from ozone exposed and control mice. Ozone acutely induced AHR to CCh. Dexamethasone or indomethacin had little effect on the ozone-induced AHR; while, ABT, a cytochrome P450 inhibitor, markedly attenuated airway sensitivity. BAL fluid from ozone exposed animals, which did not contain an increase in neutrophils or interleukin (IL)-6 levels, increased airway sensitivity following in vitro incubation with a naïve PCLS. In parallel, significant increases in oxidized lipids were also identified using LC-MS with increases of 20-HETE that were decreased following ABT treatment.

Conclusions/Significance

These data show that ozone acutely induces AHR to CCh independent of inflammation and is insensitive to steroid treatment or cyclooxygenase (COX) inhibition. BAL fluid from ozone exposed mice mimicked the effects of in vivo ozone exposure that were associated with marked increases in oxidized lipids. 20-HETE plays a pivotal role in mediating acute ozone-induced AHR.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.     

Heavy Metal (Hg,Cr, Cd,and Pb) Contamination in Urban Areas and Wildlife Reserves: Honeybees as Bioindicators

The degree of heavy metal (Hg, Cr, Cd, and Pb) pollution in honeybees (Apis mellifera) was investigated in several sampling sites around central Italy including both polluted and wildlife areas. The honeybee readily inhabits all environmental compartments, such as soil, vegetation, air, and water, and actively forages the area around the hive. Therefore, if it functions in a polluted environment, plant products used by bees may also be contaminated, and as a result, also a part of these pollutants will accumulate in the organism. The bees, foragers in particular, are good biological indicators that quickly detect the chemical impairment of the environment by the high mortality and the presence of pollutants in their body or in beehive products. The experiment was carried out using 24 colonies of honeybees bred in hives dislocated whether within urban areas or in wide countryside areas. Metals were analyzed on the foragers during all spring and summer seasons, when the bees were active. Results showed no presence of mercury in all samples analyzed, but honeybees accumulated several amounts of lead, chromium, and cadmium. Pb reported a statistically significant difference among the stations located in urban areas and those in the natural reserves, showing the highest values in honeybees collected from hives located in Ciampino area (Rome), next to the airport. The mean value for this sampling station was 0.52 mg kg⁻¹, and July and September were characterized by the highest concentrations of Pb. Cd also showed statistically significant differences among areas, while for Cr no statistically significant differences were found.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013

This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross‐tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.     

Carbazole-containing arylcarboxamides as BACE1 inhibitors

β-Secretase (BACE1) is widely recognized as a prime drug target for the treatment of Alzheimer's disease (AD). In this Letter, we report the synthesis and the BACE1 inhibitory activity of novel, variously substituted N-[3-(9H-carbazol-9-yl)-2-hydroxypropyl]-arylcarboxamides. The best results have been obtained with the introduction of a 4-OMe substituent (IC(50)=3.8 μM) or a 3,4-dichloro substituent (IC(50)=2.5 μM) in the amidic aromatic ring. The blood-brain barrier penetration predictions resulted to be promising for this type of compounds. To better understand the structure-activity relationships (SAR) of the new derivatives, a docking study procedure has been applied exploiting different conformational and ionic states of BACE1.     

Striatal glutamate release evoked in vivo by NMDA is dependent upon ongoing neuronal activity in the substantia nigra, endogenous striatal substance P and dopamine

The aim of the present microdialysis study was to investigate whether the increase in striatal glutamate levels induced by intrastriatal perfusion with NMDA was dependent on the activation of extrastriatal loops and/or endogenous striatal substance P and dopamine. The NMDA-evoked striatal glutamate release was mediated by selective activation of the NMDA receptor-channel complex and action potential propagation, as it was prevented by local perfusion with dizocilpine and tetrodotoxin, respectively. Tetrodotoxin and bicuculline, perfused distally in the substantia nigra reticulata, prevented the NMDA-evoked striatal glutamate release, suggesting its dependence on ongoing neuronal activity and GABA(A) receptor activation, respectively, in the substantia nigra. The NMDA-evoked glutamate release was also dependent on striatal substance P and dopamine, as it was antagonized by intrastriatal perfusion with selective NK(1) (SR140333), D(1)-like (SCH23390) and D(2)-like (raclopride) receptor antagonists, as well as by striatal dopamine depletion. Furthermore, impairment of dopaminergic transmission unmasked a glutamatergic stimulation by submicromolar NMDA concentrations. We conclude that in vivo the NMDA-evoked striatal glutamate release is mediated by activation of striatofugal GABAergic neurons and requires activation of striatal NK(1) and dopamine receptors. Endogenous striatal dopamine inhibits or potentiates the NMDA action depending on the strength of the excitatory stimulus (i.e. the NMDA concentration).     

The second-agent effect: communicative gestures increase the likelihood of perceiving a second agent

Background

Beyond providing cues about an agent''s intention, communicative actions convey information about the presence of a second agent towards whom the action is directed (second-agent information). In two psychophysical studies we investigated whether the perceptual system makes use of this information to infer the presence of a second agent when dealing with impoverished and/or noisy sensory input.

Methodology/Principal Findings

Participants observed point-light displays of two agents (A and B) performing separate actions. In the Communicative condition, agent B''s action was performed in response to a communicative gesture by agent A. In the Individual condition, agent A''s communicative action was replaced with a non-communicative action. Participants performed a simultaneous masking yes-no task, in which they were asked to detect the presence of agent B. In Experiment 1, we investigated whether criterion c was lowered in the Communicative condition compared to the Individual condition, thus reflecting a variation in perceptual expectations. In Experiment 2, we manipulated the congruence between A''s communicative gesture and B''s response, to ascertain whether the lowering of c in the Communicative condition reflected a truly perceptual effect. Results demonstrate that information extracted from communicative gestures influences the concurrent processing of biological motion by prompting perception of a second agent (second-agent effect).

Conclusions/Significance

We propose that this finding is best explained within a Bayesian framework, which gives a powerful rationale for the pervasive role of prior expectations in visual perception.     

Genetic diversity and relationships of endangered Spanish cattle breeds

Information on the genetic structure and variability of autochthonous livestock breeds is essential for effective conservation programs. Here we present a molecular characterization on the basis of 30 microsatellite markers of 5 Spanish endangered cattle breeds Betizu (BET), Mallorquina (MAL), Menorquina, Monchina (MON), and Serrana de Teruel (ST) and of 2 fighting bull populations, Casta Navarra (CN) and Casta Vistahermosa. The feral and critically endangered BET is divided into 2 subpopulations, one of which has exceptionally low diversity values. A low number of alleles was also observed in the island population MAL. Although the small population size and genetic drift have caused a considerable divergence between the breeds, phylogenetic analysis is in accordance with historical and geographical data. The 2 northern Spanish feral breeds BET and MON cluster together. The local fighting breed CN is relatively close to the more inbred Casta Vistahermosa, which is the progenitor of most other fighting bulls in Spain. Comparison with nonendangered breeds suggests admixture of Alpine and/or Pyrenean mountain cattle in the ST, which may contribute to the high level of linkage disequilibrium in this population.     

Following the Tracks of the First South Americans

In this article, a summary of the geologic, paleontological, and human history of an area of the Atlantic coast in the Pampean plain, Argentina is discussed. This area presents very interesting characteristics. On the one hand, the area includes the Monte Hermoso cliffs studied by Charles Darwin in 1832, which compose the set of localities related to the development of the theory of evolution. On the other hand, in the referred area, an extraordinary amount of human and Pleistocene mammal footprints are registered. Also in that section, four diachronic stages have been registered which depict the evolutionary scenario during the last five million years. Four paleontological and archeological sites are described, showing the palaeoenvironmental changes that occurred there regarding fauna associations and human settlement. The first scenario is found at Monte Hermoso cliff, whose sediments contain fossil remains of the autochthonous South American fauna. The second scenario shows a remarkable change in the drainage system where the fauna is composed of immigrated taxa due to the Great American Biotic Interchange. Both last scenarios show human presence; the third one shows faint evidences (one human trackway and two isolated footprints), and in the last one the hunter–gatherers are fully represented as a well-established population on the Pampean coast during the Early Holocene, registered at La Olla and Monte Hermoso I sites. In this way, the sites summarized in this work allow the reconstruction of four remarkable evolutionary scenarios in South America, as regards landscapes, fauna associations, and human population.