Deep Experimental Profiling of microRNA Diversity, Deployment, and Evolution Across the \u3ci\u3eDrosophila\u3c/i\u3e Genus

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution

Deep Experimental Profiling of MicroRNA Diversity, Deployment, and Evolution Across the \u3ci\u3eDrosphila\u3c/i\u3e Genus

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution

Cost-effectiveness of collaborative care for chronically ill patients with comorbid depressive disorder in the general hospital setting, a randomised controlled trial

Background. Depressive disorder is one of the most common disorders, and is highly prevalent in chronically ill patients. The presence of comorbid depression has a negative influence on quality of life, health care costs, self-care, morbidity, and mortality. Early diagnosis and well-organized treatment of depression has a positive influence on these aspects. Earlier research in the USA has reported good results with regard to the treatment of depression with a collaborative care approach and an antidepressant algorithm. In the UK 'Problem Solving Treatment' has proved to be feasible. However, in the general hospital setting this approach has not yet been evaluated. Methods/Design. CC: DIM (Collaborative Care: Depression Initiative in the Medical setting) is a two-armed randomised controlled trial with randomisation at patient level. The aim of the trial is to evaluate the treatment of depressive disorder in general hospitals in the Netherlands based on a collaborative care framework, including contracting, 'Problem Solving Treatment', antidepressant algorithm, and manual-guided self-help. 126 outpatients with diabetes mellitus, chronic obstructive pulmonary disease, or cardiovascular diseases will be randomised to either the intervention group or the control group. Patients will be included if they have been diagnosed with moderate to severe depression, based on the DSM-IV criteria in a two-step screening method. The intervention group will receive treatment based on the collaborative care approach; the control group will receive 'care as usual'. Baseline and follow-up measurements (after 3, 6, 9, and 12 months) will be performed by means of questionnaires. The primary outcome measure is severity of depressive symptoms, as measured with the PHQ-9. The secondary outcome measure is the cost-effectiveness of these treatments according to the TiC-P, the EuroQol and the SF-36. Discussion. Earlier research has indicated that depressive disorder is a chronic, mostly recurrent illness, which tends to cluster with physical comorbidity. Even though the treatment of depressive disorder based on the guidelines for depression is proven effective, these guidelines are often insufficiently adhered to. Collaborative care and 'Problem Solving Treatment' will be specifically tailored to patients with depressive disorders and evaluated in a general hospital setting in the Netherlands

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Replication Fork Stability Confers Chemoresistance in BRCA-deficient Cells

Brca1- and Brca2-deficient cells have reduced capacity to repair DNA double-strand breaks (DSBs) by homologous recombination (HR) and consequently are hypersensitive to DNA damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3/4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore HR activity at DSBs. Instead, its absence inhibits the recruitment of the MRE11 nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation. More generally, acquisition of PARPi and cisplatin resistance is associated with replication fork (RF) protection in Brca2-deficient tumor cells that do not develop Brca2 reversion mutations. Disruption of multiple proteins, including PARP1 and CHD4, leads to the same end point of RF protection, highlighting the complexities by which tumor cells evade chemotherapeutic interventions and acquire drug resistance

Suoli contaminati da As: l’importanza di speciazione e biodisponibilità per la valutazione del rischio reale

Qual è il rischio per la salute umana nell‟impiego di suoli contaminati da arsenico (As) in agricoltura o per il pascolo? Come è noto, non è tanto la concentrazione totale del contaminante a costituire di per sé una minaccia, quanto la sua distribuzione nelle diverse forme chimiche (speciazione), che ne influenza la frazione biodisponibile e quindi le sue possibilità di entrare nella filiera alimentare. E‟ in questa direzione che si muove il presente lavoro, volto a determinare il rischio reale che deriva dalla presenza di As in suoli campionati in aree pertinenti ad ex attività industriali (Scarlino, GR) e minerarie (Valle Anzasca, VB), con concentrazioni tra le decine ad alcune migliaia di ppm. È così stato adottato un duplice approccio, mirato ad ottenere da un lato una puntuale caratterizzazione chimico-mineralogica dei suoli stessi e quindi informazioni circa la speciazione dell‟As, dall‟altro a valutarne la biodisponibilità e l‟ecotossicità. Le analisi chimiche e mineralogiche dei suoli sono effettuate mediante tecniche che impiegano radiazione X; in particolare la caratterizzazione chimica in situ viene condotta tramite spettrometria di fluorescenza portatile con rivelatore a dispersione di energia (ED-pXRF), e in laboratorio mediante dispersione di lunghezza d‟onda (WD-XRF). In via preliminare esse hanno permesso di individuare nei suoli di Valle Anzasca una certa correlazione tre le concentrazioni rispettivamente di As e Fe e di As e S. La caratterizzazione mineralogica è invece condotta con un diffrattometro di raggi X su polvere (XRPD), introducendo corindone (Al2O3) come standard interno per la quantitativa. Non sono stati però rivelati minerali dell‟As, per via della loro scarsa concentrazione. Anche a questo proposito, sono in atto procedure di estrazione sequenziale (metodo Wenzel), per valutare la maggiore o minore mobilità dell‟As, ma pure ottenere informazioni complementari circa i minerali dell‟As presenti (ad esempio è stato individuato pentossido di As in un campione di Scarlino). Ulteriori dati circa la distribuzione dell‟As nei suoli vengono ottenuti per mezzo di una microfluorescenza di raggi X (ED-μXRF), effettuando scansioni dei suoli in sezione sottile. La biodisponibilità viene valutata utilizzando lombrichi epigeici della specie Eisenia andrei (Bouché), esposti a microcosmi contaminati e sottoposti ad analisi dei fluidi celomatici mediante TXRF e della distribuzione dell‟elemento nel corpo mediante ED-μXRF

TXRF analysis of earthworm coelomic fluid extracts: a useful tool to assess the bioavailability of As in soils

Arsenic (As) is a metalloid often associated to mining and industrial sites and its presence can cause health problems to living organisms and human beings. In order to assess As bioavailability in soils, tests which use earthworms as sentinel organisms are usually done. The evaluation of As concentration in the earthworm is commonly done after the whole digestion of the organism, which can lead to the overestimation of the concentration due to the possible presence of soil residues in the intestine. However, As is mainly accumulated by earthworms in the coelomic cavity , in particular in the coelomic fluid. This fluid can be easily extracted without killing the organism and analysed. Due to its small amount (less than 100 microliters), total x-ray fluorescence spectroscopy (TXRF) has demonstrated to be a powerful method for As detection in coelomic fluid extracts [1]. For these reasons, the present work aims at developing a new method to assess As bioavailability in contaminated soils by analyzing the As concentration in coelomic fluid extracts with TXRF. Six natural As polluted soils and two control soils were characterized by XRPD and WDXRF, while the As mobility was assessed by a sequential extraction procedure. Then, 10 sexually mature earthworms were exposed to each soil for 14 days. The elemental distribution inside the earthworm was studied by μXRF on thin sections, which localized As only in the coelomic cavity. After 24h without nourishment, three earthworms per soil were washed with distilled water and coelomic fluid extracts were collected from each of them applying a voltage of 5 V for 3 seconds. Ten microliters of extract were mixed with 80 µl of PVA and 10 µl of Y standard solution (10 mg/l). In order to compare the As concentration in the coelomic fluid extracts with the As concentration in the earthworm body, additional three earthworms per soil were depurated, dryed at 60 °C and pulverized. Slurry suspensionswere prepared using 100 mg of powder, 5 ml of Triton X-100 and 10 µl of Y standard solution (1000 mg/l). In both cases, 10 µl of sample were pipetted onto a quartz reflector and were left drying at 50 °C. TXRF analysis were performed with a S2 Picofox spectrometer (Bruker) using an acquisition time of 1000 s. Results revealed that As (both in fluids and whole bodies) increased with increasing mobile As in the soil. hHowever, As saturation (in both fluid and body) was observed when the mobile As fraction exceeded 200 mg/kg. Finally, the As concentration in coelomic fluids was positively correlated with that in the whole body. These results show that TXRF is a powerful tool to determine As concentration in earthworm coelomic fluids and that it can be used for As bioavailbility studies in soils. [1] I. Allegretta, C. Porfido, O. Panzarino, M.C. Fontanella, G.M. Beone, M. Spagnuolo, R. Terzano, Spectrochimica Acta Part B 130, 2017, 21-25

End-stage heart failure: Two surgical approaches with different rehabilitative outcomes

Background A rising number of patients are surgically treated for heart failure at the more advanced stage, thanks to the increasing use of left ventricular assist device (LVAD) as a reliable alternative to heart transplantation (HTx). However, it is still unknown whether differences exist between the two surgical approaches in the efficacy of rehabilitation programmes. Therefore, aim of this study was to evaluate whether functional capacity and rehabilitative outcomes differ between HTx and implantation of LVAD. Methods and results We enrolled 51 patients with HTx and 46 with LVAD upon admission to our rehabilitationunit. We evaluated six-minute walking test (6MWT), resting oxygen saturation (SaO(2)) and nutritional assessment before and after a standardised cardiovascular rehabilitation programme. HTx and LVAD groups differed in age, anthropometric variables, gender distribution. Upon enrolment, 6MWT distance was similar in the two groups, whereas malnutrition was less frequent and the waist circumference/height ratio (WHtR) was greater in LVAD patients. SaO(2) was greater in HTx patients. Rehabilitation improved SaO(2), 6MWT distance and nutritional status. The difference in malnutrition disappeared, but WHtR remained higher in the LVAD and SaO(2) higher in the HTx patients; the 6MWT distance improved more in the HTx patients. Multivariate linear regression analysis confirmed that the type of intervention was independent predictor of 6MWT distance after rehabilitation. Conclusions HTx patients improve more rapidly and perform better after rehabilitation, suggesting the need for more tailored rehabilitation training for LVAD patients

The Challenge of Pharmacotherapy in Children and Adolescents with Epilepsy-ADHD Comorbidity

Epilepsy is common in children and adolescents where its prevalence is 3.2-5.5/1000. About one-third of patients also have attention deficit hyperactivity/impulsivity disorder (ADHD). The possible relationship between epilepsy and ADHD is still unclear, and ADHD symptoms (such as inattention, hyperactivity, behavioral disturbances) are frequently considered as adverse effects of antiepileptic drugs (AEDs). The literature was searched for data on the behavioral effects of AEDs. Phenobarbital is the most frequently reported medication to induce symptoms of ADHD, followed by topiramate and valproic acid. Phenytoin seems to exert modest effects, while for levetiracetam there are contrasting data. Lacosamide induces some beneficial effects on behavior; carbamazepine and lamotrigine exert favorable effects on attention and behavior. Gabapentin and vigabatrin have limited adverse effects on cognition. Oxcarbazepine, rufinamide, and eslicarbazepine do not seem to aggravate or induce ADHD symptoms, whereas perampanel can lead to a high incidence of hostile/aggressive behavior, which increases with higher dosages. Information about the behavioral effects of ethosuximide, zonisamide, tiagabine, pregabalin, stiripentol, and retigabine is still limited. Because ADHD significantly affects the quality of life of epilepsy patients, the clinical management of this neuropsychiatric disorder should be a priority. Methylphenidate is effective most children and adolescents with ADHD symptoms and comorbid epilepsy, without a significant increase of seizure risk, although data are still limited with few controlled trials