Eukaryotic snoRNAs: a paradigm for gene expression flexibility.

AbstractSmall nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs – to guide site-specific rRNA modification – is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes

Species-Specific Effects of Cation Channel TRPM4 Small-Molecule Inhibitors

Background: The Transient Receptor Potential Melastatin member 4 (TRPM4) gene encodes a calcium-activated non-selective cation channel expressed in several tissues. Mutations in TRPM4 have been reported in patients with different types of cardiac conduction defects. It is also linked to immune response and cancers, but the associated molecular mechanisms are still unclear. Thus far, 9-phenanthrol is the most common pharmacological compound used to investigate TRPM4 function. We recently identified two promising aryloxyacyl-anthranilic acid compounds (abbreviated CBA and NBA) inhibiting TRPM4. However, all aforementioned compounds were screened using assays expressing human TRPM4, whereas the efficacy of mouse TRPM4 has not been assessed. Mouse models are essential to investigate ion channel physiology and chemical compound efficacy. Aim: In this study, we performed comparative electrophysiology experiments to assess the effect of these TRPM4 inhibitors on human and mouse TRPM4 channels heterologously expressed in TsA-201 cells. Methods and Results: We identified striking species-dependent differences in TRPM4 responses. NBA inhibited both human and mouse TRPM4 currents when applied intracellularly and extracellularly using excised membrane patches. CBA inhibited human TRPM4, both intracellularly and extracellularly. Unexpectedly, the application of CBA had no inhibiting effect on mouse TRPM4 current when perfused on the extracellular side. Instead, its increased mouse TRPM4 current at negative holding potentials. In addition, CBA on the intracellular side altered the outward rectification component of the mouse TRPM4 current. Application of 9-phenanthrol, both intracellularly and extracellularly, inhibited human TRPM4. For mouse TRPM4, 9-phenanthrol perfusion led to opposite effects depending on the site of application. With intracellular 9-phenanthrol, we observed a tendency towards potentiation of mouse TRPM4 outward current at positive holding potentials. Conclusion: Altogether, these results suggest that pharmacological compounds screened using “humanised assays” should be extensively characterised before application in vivo mouse models

Species-specific effects of cation channel TRPM4 small-molecule inhibitors

Background The Transient Receptor Potential Melastatin member 4 (TRPM4) gene encodes a calcium-activated non-selective cation channel expressed in several tissues. Mutations in TRPM4 have been reported in patients with different types of cardiac conduction defects. It is also linked to immune response and cancers, but the associated molecular mechanisms are still unclear. Thus far, 9-phenanthrol is the most common pharmacological compound used to investigate TRPM4 function. We recently identified two promising aryloxyacyl-anthranilic acid compounds (abbreviated CBA and NBA) inhibiting TRPM4. However, all afore-mentioned compounds were screened using assays expressing human TRPM4, whereas the efficacy on mouse TRPM4 has not been assessed. Mouse models are essential to investigate ion channel physiology and chemical compound efficacy. Aim In this study, we performed comparative electro-physiology experiments to assess the effect of these TRPM4 inhibitors on human and mouse TRPM4 channels heterologously expressed in TsA-201 cells. Methods and Results We identified striking species-dependent differences in TRPM4 responses. NBA inhibited both human and mouse TRPM4 currents when applied intracellularly and extracellularly using excised membrane patches. CBA inhibited human TRPM4, both intracellularly and extracellularly. Unexpectedly, the application of CBA had no inhibiting effect on mouse TRPM4 current when perfused on the extracellular side. Instead, it increased mouse TRPM4 current at negative holding potentials. In addition, CBA on the intracellular side altered the outward rectification component of the mouse TRPM4 current. Application of 9-phenanthrol, both intracellularly and extracellularly, inhibited human TRPM4. For mouse TRPM4, 9-phenanthrol perfusion led to opposite effects depending on the site of application. With intracellular 9-phenanthrol, we observed a tendency towards potentiation of mouse TRPM4 outward current at positive holding potentials. Conclusion Altogether, these results suggest that pharmacological compounds screened using “humanised assays” should be extensively characterised before application in in vivo mouse models

Nature-Inspired Processes and Structures: New Paradigms to Develop Highly Bioactive Devices for Hard Tissue Regeneration

Material scientists are increasingly looking to natural structures as inspiration for new-generation functional devices. Particularly in the medical field, the need to regenerate tissue defects claims, since decades, biomaterials with the ability to instruct cells toward formation and organization of new tissue. It is today increasingly accepted that biomimetics is a leading concept for biomaterials development. In fact, there is increasing evidence that the use of biomedical devices showing substantial mimicry of the composition and multi-scale structure of target native tissues have enhanced regenerative ability. As a relevant example, biomimetic materials have high potential to solve degenerative diseases affecting the musculoskeletal system, namely, bone, cartilage and articular tissues, which is of pivotal importance for most of human abilities, such as walking, running, manipulating, and chewing. In this respect, the adoption of nature-inspired processes and structures is an emerging fabrication concept, uniquely able to provide biomaterials with superior biological performance. The chapter will give an overview of the most recent results obtained in the field of hard tissue regeneration by using 3D biomaterials obtained by nature-inspired approaches. The main focus is given to porous hydroxyapatite-based ceramic or hybrid scaffolds for regeneration of bone and osteochondral tissues in neurosurgery and orthopedics

Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor.

Despite being among the most characterized G protein-coupled receptors (GPCRs), adenosine receptors (ARs) have always been a difficult target in drug design. To date, no agonist other than the natural effector and the diagnostic regadenoson has been approved for human use. Recently, the structure of the adenosine A1 receptor (A1R) was determined in the active, Gi protein complexed state; this has important repercussions for structure-based drug design. Here, we employed supervised molecular dynamics simulations and mutagenesis experiments to extend the structural knowledge of the binding of selective agonists to A1R. Our results identify new residues involved in the association and dissociation pathway, they suggest the binding mode of N6-cyclopentyladenosine (CPA) related ligands, and they highlight the dramatic effect that chemical modifications can have on the overall binding mechanism, paving the way for the rational development of a structure-kinetics relationship of A1R agonists.Leverhulme Trus

Targeting Ion Channel TRPM4

The transient receptor potential melastatin 4 (TRPM4) ion channel is ubiquitously expressed. Dysregulation and/or functional mutations of TRPM4 lead to several diseases. Within our studies, we screened for TRPM4 inhibitors and identified small molecules that block TRPM4 in the low µM range. Furthermore, we investigated the pathophysiology of TRPM4 in cardiac conditions, immune diseases and cancer using these novel inhibitors, molecular biology techniques and functional assays

Many Labs 5:Testing pre-data collection peer review as an intervention to increase replicability

Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3?9; median total sample = 1,279.5, range = 276?3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (?r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00?.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19?.50)

Prospettive e potenzialità della digitalizzazione del settore forestale in Italia

Information and Communication Technologies (ICT) play a key role for improving the implementation of sustainable forest management at local, regional, and global level. The ICT potential to easily exploit a wider and more up-to-date set of information on the economic, environmental, and so- cial value of forests is of relevant help for the daily work of technicians, land owners, and companies in boosting the efficiency and effectiveness of forest management. The concept of “Precision Forestry” (PF) was developed from the early 2000s, as a branch of precision farming or precision agriculture. PF includes the use of ICT, remote and proximal sensing technologies, and other devices to coordinate and control several processes on a spatial scale (“Precision”) for monitoring, planning, and managing forest resources (“Forestry”). The aim of this monography is to collect and describe some of the most important PF experiences applied or potential- ly useful for the Italian forestry sector. It may represent a reference guide for the stakeholders, such as forest owners, professional technicians, public administrators, and policy makers. The book includes eleven chapters reviewing the main tech- nological tools available in the Italian context and the most recent advances of ICT in forestry, also focusing on the strengths and weaknesses of their practical implementation. The opportunities and challenges of implementing PF meth- ods, practices and technologies are also discussed. In the first two chapters the precision forestry concept and its historical development are introduced. In the third chap- ter some basic elements of ICT, GIS, Global Navigation Satellite Systems (GNSS), remote/proximal sensing, and related technologies which are essential for a better compre- hension of PF applications are recalled. In chapter 4 recent advances in large scale forest inventories with a focus on mapping and on the spatial estimation of forest variables integrating field surveys and multisource re- motely sensed data are described. Current advancements in the acquisition of field information including Terrestrial La- ser Scanning (TLS), new digital dendrometers, tree-talkers, terrestrial cameras, and APP for portable devices such as smartphones or tablets for dendrometric tree measures and new citizen science applications to support quantitative and qualitative spatial estimation of forest variables over large areas (i.e., forest health, fuel types) are also presented. The chapter ends up with the description of some experiences in the implementation of Forest Information Systems in Italy to provide a simple open-access to such new generation of spatial forest information. In chapter 5 PF tools, instruments, and technologies to sup- port sustainable forest management are illustrated. APPs developed to acquire field plots data to simulate manage- ment operations, the application of photogrammetric tech- nologies from Unmanned Aerial Vehicles and TLS data for monitoring with high-spatial scale forest monitoring and for acquiring indicators at single tree level are presented. A de- tailed description of new user-friendly tools for forest roadplanning, design and construction, as well as forest opera- tion planning is also included. Precision forest tree farming (with particular reference to poplar cultivation), useful to promote and increase the prof- itability and sustainability of forest plantations within the Italian context is described in chapter 6. The innovation and enhancement within the supply chain of wood plantations (from planting to harvesting, including monitoring and identification of stress) by soil proximal sensing techniques, Early Warning Systems, and specific software are highlight- ed. Considering the even higher market demands, promoted by the large-scale planting programs for climate changes mit- igation and the demands for propagation material for en- vironmental recovery, innovative techniques and methods supported by ICT in the forest nursery sector are described in chapter 7. In chapter 8 available technologies related to precision har- vesting are analyzed and described taking into consideration the wood chain efficiency, by means of improved commu- nications between the owner/buyer and operators as well as among machineries used in forest operations, health and safety of forest operators, environmental impacts mitigation and recovery, and operators training. Advanced communi- cation systems and sensors for the exchange of data and information between machines, machine-equipments and/or machine-operators, teleoperations and automation are also described. Chapters 9 and 10 are related to wood products traceabil- ity, timber quality assessment as well as the technologies for the optimization of wood transformation processes. The concepts of wood product traceability and tracing, togeth- er with latest digital technologies for the identification and tracking of the logs (i.e., fingerprinting and RFID), are de- tailly reported. Chapter 11 is finally dedicated to the relationship between the EU policy framework and the digitalization process in both agricultural and forestry sectors. The book summarizes, under a proactive and homogeneous framework, PF methods, tools and technologies in relation with the digital transition of the Italian forestry sectors. The authors hope this book will be useful for improving the implementation of sustainable forest management practic- es at all levels in Italy, providing a comprehensive review useful for policy makers, technicians, forestry owners and students