Transnational strategy on the sustainable management and responsible use of non-native trees in the Alpine Space

Abstract Non-native tree species – defined as those species intentionally or unintentionally introduced by humans – have long been a part of the Alpine Space, providing numerous benefits, but also posing a potential threat to native biodiversity and related ecosystem services. Compared to the urban space where non-native trees comprise most tree species, the number of non-native trees in forests and plantations is relatively low. To evaluate potential risks and benefits of non-native trees in the Alpine Space, a transnational strategy for the responsible use and management of non-native trees is needed. The goals of the strategy are to tailor management practices for a sustainable and responsible use or admixture of non-native trees, to reduce the risks connected with the invasive potential of some non-native tree species, to help forests and urban areas to adapt to climate change, and to improve coordination and cooperation regarding best practices between different regions of the Alpine Space. A proposal was developed in a four-step process including expert-based assessment, stakeholder mapping, an extensive data review, and a public consultation. For implementing the strategy fully, strong collaboration among diverse stakeholders is anticipated and robust governance and an adequate long-term and fair funding scheme is needed

Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots

International audiencePredicting the folding of an RNA sequence, while allowing general pseudoknots (PK), consists in finding a minimal free-energy matching of its $n$ positions. Assuming independently contributing base-pairs, the problem can be solved in $\Theta(n^3)$-time using a variant of the maximal weighted matching. By contrast, the problem was previously proven NP-Hard in the more realistic nearest-neighbor energy model. In this work, we consider an intermediate model, called the stacking-pairs energy model. We extend a result by Lyngs\o, showing that RNA folding with PK is NP-Hard within a large class of parametrization for the model. We also show the approximability of the problem, by giving a practical $\Theta(n^3)$ algorithm that achieves at least a $5$-approximation for any parametrization of the stacking model. This contrasts nicely with the nearest-neighbor version of the problem, which we prove cannot be approximated within any positive ratio, unless $P=NP$.La prédiction du repliement, avec pseudonoeuds généraux, d'une séquence d'ARN de taille $n$ est équivalent à la recherche d'un couplage d'énergie libre minimale. Dans un modèle d'énergie simple, où chaque paire de base contribue indépendamment à l'énergie, ce problème peut être résolu en temps $\Theta(n^3)$ grâce à une variante d'un algorithme de couplage pondéré maximal. Cependant, le même problème a été démontré NP-difficile dans le modèle d'énergie dit des plus proches voisins. Dans ce travail, nous étudions les propriétés du problème sous un modèle d'empilements, constituant un modèle intermédiaire entre ceux d'appariement et des plus proches voisins. Nous démontrons tout d'abord que le repliement avec pseudo-noeuds de l'ARN reste NP-difficile dans de nombreuses valuations du modèle d'énergie. . Par ailleurs, nous montrons que ce problème est approximable, en proposant un algorithme polynomial garantissant une $1/5$-approximation. Ce résultat illustre une différence essentielle entre ce modèle et celui des plus proches voisins, pour lequel nous montrons qu'il ne peut être approché à aucun ratio positif par un algorithme en temps polynomial sauf si $N=NP$

RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference

Eukaryotic cap-dependent mRNA translation is mediated by the initiation factor eIF4E, which binds mRNAs and stimulates efficient translation initiation. eIF4E is often overexpressed in human cancers. To elucidate the molecular signature of eIF4E target mRNAs, we analyzed sequence and structural properties of two independently derived polyribosome recruited mRNA datasets. These datasets originate from studies of mRNAs that are actively being translated in response to cells over-expressing eIF4E or cells with an activated oncogenic AKT: eIF4E signaling pathway, respectively. Comparison of eIF4E target mRNAs to mRNAs insensitive to eIF4E-regulation has revealed surprising features in mRNA secondary structure, length and microRNA-binding properties. Fold-changes (the relative change in recruitment of an mRNA to actively translating polyribosomal complexes in response to eIF4E overexpression or AKT upregulation) are positively correlated with mRNA G+C content and negatively correlated with total and 3′UTR length of the mRNAs. A machine learning approach for predicting the fold change was created. Interesting tendencies of secondary structure stability are found near the start codon and at the beginning of the 3′UTR region. Highly upregulated mRNAs show negative selection (site avoidance) for binding sites of several microRNAs. These results are consistent with the emerging model of regulation of mRNA translation through a dynamic balance between translation initiation at the 5′UTR and microRNA binding at the 3′UTR

Engineering cooperative tecto–RNA complexes having programmable stoichiometries

High affinity and specificity RNA–RNA binding interfaces can be constructed by combining pairs of GNRA loop/loop–receptor interaction motifs. These interactions can be fused using flexible four-way junction motifs to create divalent, self-assembling scaffolding units (‘tecto-RNA’) that have favorable properties for nanomedicine and other applications. We describe the design and directed assembly of tecto-RNA units ranging from closed, cooperatively assembling ring-shaped complexes of programmable stoichiometries (dimers, trimers and tetramers) to open multimeric structures. The novelty of this work is that tuning of the stoichiometries of self-assembled complexes is achieved by precise positioning of the interaction motifs in the monomer units rather than changing their binding specificities. Structure-probing and transmission electron microscopy studies as well as thermodynamic analysis support formation of closed cooperative complexes that are highly resistant to nuclease digestion. The present designs provide two helical arms per RNA monomer for further functionalization aims

Effects of total laryngectomy on olfactory function, health-related quality of life, and communication: a 3-year follow-up study

<p>Abstract</p> <p>Background</p> <p>As total laryngectomy results in loss of airflow through the nose, one of the adverse effects for a majority of patients is the reduced or complete loss of olfactory function. However, with the introduction of a new method, the Nasal Airflow-Inducing Maneuver (NAIM), an important technique is available for laryngectomized patients to regain the ability to smell. The purpose of the present study was to assess changes in olfaction, health-related quality of life (HRQL) and communication 3 years after NAIM rehabilitation.</p> <p>Methods</p> <p>18 patients (15 men and 3 women; mean age, 71 years) who had undergone laryngectomy and NAIM rehabilitation were followed longitudinally for 3 years. For comparison an age and gender matched control group with laryngeal cancer treated with radical radiotherapy was included. Olfactory function was assessed using the Questionnaire on Odor, Taste and Appetite and the Scandinavian Odor Identification Test. HRQL was assessed by: 1) the European Organization for Research and Treatment for cancer quality of life questionnaires; and 2) the Hospital Anxiety and Depression Scale. Communication was assessed by the Swedish Self-Evaluation of Communication Experiences after Laryngeal Cancer. Descriptive statistics with 95% confidence interval were calculated according to standard procedure. Changes over time as well as tests between pairs of study patients and control patients were analyzed with the Fisher nonparametric permutation test for matched pairs.</p> <p>Results</p> <p>Thirty-six months after rehabilitation 14 of 18 laryngectomized patients (78%) were smellers. There were, with one exception (sleep disturbances), no clinically or statistically significant differences between the study and the control group considering HRQL and mental distress. However, statistical differences (p < 0.001) were found between the study and the control group concerning changes in communication.</p> <p>Conclusion</p> <p>Olfactory training with NAIM should be integrated into the multidisciplinary rehabilitation program after total laryngectomy. Our study shows that patients who were successfully rehabilitated concerning olfaction and communication had an overall good HRQL and no mental distress. Moreover, the EORTC questionnaires should be complemented with more specific questionnaires when evaluating olfaction and communication in laryngectomized patients.</p

Transnational strategy on the sustainable management and responsible use of non-native trees in the Alpine Space

Non-native tree species – defined as those species intentionally or unintentionally introduced by humans – have longbeen a part of the Alpine Space, providing numerous benefits, but also posing a potential threat to native biodiversityand related ecosystem services. Compared to the urban space where non-native trees comprise most tree species,the number of non-native trees in forests and plantations is relatively low. To evaluate potential risks and benefits ofnon-native trees in the Alpine Space, a transnational strategy for the responsible use and management of non-nativetrees is needed. The goals of the strategy are to tailor management practices for a sustainable and responsible useor admixture of non-native trees, to reduce the risks connected with the invasive potential of some non-native treespecies, to help forests and urban areas to adapt to climate change, and to improve coordination and cooperationregarding best practices between different regions of the Alpine Space. A proposal was developed in a four-stepprocess including expert-based assessment, stakeholder mapping, an extensive data review, and a public consulta-tion. For implementing the strategy fully, strong collaboration among diverse stakeholders is anticipated and robustgovernance and an adequate long-term and fair funding scheme is needed

Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts

Sustainably managed non-native trees deliver economic and societal benefits with limited risk of spread to adjoining areas. However, some plantations have launched invasions that cause substantial damage to biodiversity and ecosystem services, while others pose substantial threats of causing such impacts. The challenge is to maximise the benefits of non-native trees, while minimising negative impacts and preserving future benefits and options. A workshop was held in 2019 to develop global guidelines for the sustainable use of non-native trees, using the Council of Europe – Bern Convention Code of Conduct on Invasive Alien Trees as a starting point. The global guidelines consist of eight recommendations: 1) Use native trees, or non-invasive non-native trees, in preference to invasive non-native trees; 2) Be aware of and comply with international, national, and regional regulations concerning non-native trees; 3) Be aware of the risk of invasion and consider global change trends; 4) Design and adopt tailored practices for plantation site selection and silvicultural management; 5) Promote and implement early detection and rapid response programmes; 6) Design and adopt tailored practices for invasive non-native tree control, habitat restoration, and for dealing with highly modified ecosystems; 7) Engage with stakeholders on the risks posed by invasive non-native trees, the impacts caused, and the options for management; and 8) Develop and support global networks, collaborative research, and information sharing on native and non-native trees. The global guidelines are a first step towards building global consensus on the precautions that should be taken when introducing and planting non-native trees. They are voluntary and are intended to complement statutory requirements under international and national legislation. The application of the global guidelines and the achievement of their goals will help to conserve forest biodiversity, ensure sustainable forestry, and contribute to the achievement of several Sustainable Development Goals of the United Nations linked with forest biodiversity