The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes

Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.

Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods

Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.

Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP)

Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.

Outcomes among oropharyngeal and oral cavity cancer patients treated with postoperative volumetric modulated arctherapy

Background

Presently, there are few published reports on postoperative radiation therapy for oropharyngeal and oral cavity cancers treated with IMRT/VMAT technique. This study aimed to assess the oncological outcomes of this population treated with postoperative VMAT in our institution, with a focus on loco-regional patterns of failure.

Material and methods

Between 2011 and 2019, 167 patients were included (40% of oropharyngeal cancers, and 60% of oral cavity cancers). The median age was 60 years. There was 64.2% of stage IV cancers. All patients had both T and N surgery. 34% had a R1 margin, 42% had perineural invasion. 72% had a positive neck dissection and 42% extranodal extension (ENE). All patients were treated with VMAT with simultaneous integrated boost with three dose levels: 66Gy in case of R1 margin and/or ENE, 59.4-60Gy on the tumor bed, and 54Gy on the prophylactic areas. Concomittant cisplatin was administrated concomitantly when feasible in case of R1 and/or ENE.

Results

The 1- and 2-year loco-regional control rates were 88.6% and 85.6% respectively. Higher tumor stage (T3/T4), the presence of PNI, and time from surgery >45 days were significant predictive factors of worse loco-regional control in multivariate analysis (p=0.02, p=0.04, and p=0.02). There were 17 local recurrences: 11 (64%) were considered as infield, 4 (24%) as marginal, and 2 (12%) as outfield. There were 9 regional recurrences only, 8 (89%) were considered as infield, and 1 (11%) as outfield. The 1- and 2-year disease-free survival (DFS) rates were 78.9% and 71.8% respectively. The 1- and 2-year overall survival (OS) rates were 88.6% and 80% respectively. Higher tumor stage (T3/T4) and the presence of ENE were the two prognostic factors significantly associated with worse DFS and OS in multivariate analysis.

Conclusion

Our outcomes for postoperative VMAT for oral cavity and oropharyngeal cancers are encouraging, with high rates of loco-regional control. However, the management of ENE still seems challenging.

A laser-based system to heat nuclear fuel pellets at high temperature

Annealing tests are of utmost importance in nuclear fuel research, particularly to study the thermophysical properties of the material, microstructure evolution, or the released gas as a function of temperature. As an alternative to conventional furnace or induction annealing, we report on a laser-heating experiment allowing one to heat a nuclear fuel pellet made of uranium dioxide, UO2, or potentially other nuclear fuel pellets in an isothermal and controlled manner. For that purpose, we propose to use an indirect heating method based on a two compartment tungsten crucible, one containing the sample and the other acting as a laser susceptor for efficient and homogeneous heating of the assembly. With this concept, we demonstrate the heating of UO2 samples up to 1500 °C at a maximum heating rate of 30 °C/s with the use of two 500 W lasers. The system is, however, scalable to higher heating rates or higher temperatures by increasing the laser power up to few kW. The experiment has been designed to heat a pressurized water reactor fuel pellet, but the concept could be easily applied to other sample geometries or materials.

SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome

In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.

Deciphering the segregation of proteins in high-protein dairy powders after spray-drying

High-protein dairy powders are ingredients mainly produced by spray-drying, then subjected to aging during transport and storage. They often undergo physicochemical changes at this stage, such as the development of the Maillard reaction, primarily because of their intrinsic chemical properties, but also as a result of nonoptimal storage conditions. Components present at the particle surface are the first to be targeted by moisture and other environmental disruptions. Consequently, the identification, control, and prediction of particle surface components are useful to anticipate the effect of powder aging on product quality. Here, a new diafiltration method is proposed which fractionates proteins from a binary colloidal dispersion of 80% casein micelles and 20% whey proteins, according to their presence at the surface or core of the particle. This method shows that whey proteins are strongly enriched at the particle surface, whereas casein micelles are located at the core of the particles. This protocol also allows the identification of the rehydration kinetics for each rehydrated protein layer of the particle, revealing that 2 distinct forms of swelling occur: (1) a rapid swelling and elution of whey proteins present at the particle surface, and (2) a swelling of casein micelles located below the whey proteins, associated with a slow elution of casein micelles from the particles being rehydrated.

The Toll pathway mediates Drosophila resilience to Aspergillus mycotoxins through specific Bomanins

Host defense against infections encompasses both resistance, which targets microorganisms for neutralization or elimination, and resilience/disease tolerance, which allows the host to withstand/tolerate pathogens and repair damages. In Drosophila, the Toll signaling pathway is thought to mediate resistance against fungal infections by regulating the secretion of antimicrobial peptides, potentially including Bomanins. We find that Aspergillus fumigatus kills Drosophila Toll pathway mutants without invasion because its dissemination is blocked by melanization, suggesting a role for Toll in host defense distinct from resistance. We report that mutants affecting the Toll pathway or the 55C Bomanin locus are susceptible to the injection of two Aspergillus mycotoxins, restrictocin and verruculogen. The vulnerability of 55C deletion mutants to these mycotoxins is rescued by the overexpression of Bomanins specific to each challenge. Mechanistically, flies in which BomS6 is expressed in the nervous system exhibit an enhanced recovery from the tremors induced by injected verruculogen and display improved survival. Thus, innate immunity also protects the host against the action of microbial toxins through secreted peptides and thereby increases its resilience to infection.

The use of nitrous oxide 'cracking' technology in the labour ward: a case report and patient account

Nitrous oxide is a common choice of labour analgesia in many countries. However, its use is associated with significant cost to the environment as well as potential risks of long-term occupational exposure. Our hospital is one of a small number of healthcare providers in the United Kingdom trialling technology which catalytically destroys ('cracks') nitrous oxide to reduce greenhouse gas emissions and occupational exposure. When used in the setting of inhaled analgesia, cracking technology relies on capturing the patient's exhaled breath via a facemask or mouthpiece, a technique which requires some user skill and may be challenging for patients. In this report, we present the case of a primiparous 35-year-old consultant anaesthetist, who used nitrous oxide cracking technology with inhaled nitrous oxide analgesia (via a facemask) during labour. We present the patient's experiences and discuss the implications of using such technology on ambient nitrous oxide levels in the delivery room. Notably, despite this patient's professional expertise and familiarity with facemask use, nitrous oxide remained detectable throughout her labour, although generally at low levels. This illustrates that whilst this technology has the potential to reduce ambient nitrous oxide levels, its efficacy may vary depending on how it is used, with implications for patient education and support.

Current trends in craniofacial reconstruction

Reconstruction of the head and neck continues to pose a variety of difficult functional and aesthetic challenges to the plastic surgeon. While the surgical treatment for midfacial and skull base tumours continues to advance, the three-dimensional reconstruction predicaments continue to increase in complexity. Reconstructive strategies of the head and neck require the restoration of intricate skeletal architecture and large volumes of both internal and external soft tissue envelopes that can withstand adjuvant therapies. Vascularized bone grafts in combination with microsurgical techniques is the current trend of most reconstruction and has replaced local and pedicle flaps as the preferred modality for large defects. This article will focus on concise areas of difficulty in craniofacial reconstruction, including mandibular, midfacial, scalp and base of skull reconstruction. As our goals now move from flap survival to refinement, more complex and innovative reconstructions are executed. The problems with each modality are examined, and the frontiers of head and neck reconstruction are explored. With the potential combination of virtual surgery and tissue engineered biotechnology, we may someday be able to expand our reconstructive capabilities beyond free tissue transfer.

Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses

The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and translation of viral mRNAs. The first 75-80 nt, also called the leader sequence, are identical for genomic mRNA and subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the nonstructural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses, with special attention to the betacoronaviruses. The conclusions are: (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein, indicating a coevolution between the 5'UTR and NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support these conclusions and show that some conserved key residues in the amino-terminal half of the NSP1 protein are essential for evasion to the inhibitory effect of NSP1 on translation.

Viral and cellular translation during SARS‐CoV‐2 infection

SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.

Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources

Downy mildew pathogens of graminicolous hosts (Poaceae) are members of eight morphologically and phylogenetically distinct genera in the Peronosporaceae (Oomycota,Peronosporales). Graminicolous downy mildews (GDMs) cause severe losses in crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climates. In countries where the most destructive GDMs are not endemic, these organisms are often designated as high-risk foreign pathogens and subject to oversight and quarantine by regulatory officials. Thus, there is a need to reliably and accurately identify the causal organisms. This paper provides an overview of the Peronosporaceae species causing graminicolous downy mildew diseases, with a description of their impact on agriculture and the environment, along with brief summaries of the nomenclatural and taxonomic issues surrounding these taxa. Key diagnostic characters are summarized, including DNA sequence data for types and/or voucher specimens, morphological features, and new illustrations. New sequence data for cox2 and 28S rDNA markers are provided from the type specimens of three species, Peronosclerospora philippinensis, Sclerospora iseilematis, and Sclerospora northii. Thirty-nine species of graminicolous downy mildews are accepted, and seven previously invalidly published taxa are validated. Fifty-five specimens are formally designated as types, including lectotypification of 10 species, neotypification of three species, and holotype designation for Sclerophthora cryophila.

Citation: Crouch JA, Davis WJ, Shishkoff N, Castroagudín VL, Martin F, Michelmore R, Thines M (2022). Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources. Fungal Systematics and Evolution9: 43–86. doi: 10.3114/fuse.2022.09.05

Dépistage du personnel de santé exposé au SARS-CoV-2 dans un hôpital universitaire

Introduction

Dans le cadre de la pandémie mondiale au SARS-CoV-2, les personnels de santé (PS) sont professionnellement exposés à ce virus. Dans ce contexte, cette étude présente les données de surveillance de 5704 travailleurs exposés au SARS-CoV-2 d’un centre hospitalier du 17 mars au 20 avril 2020.

Matériels et méthodes

Les PS symptomatiques, les cas contacts et ceux présentant une forte anxiété ont été testés. Le diagnostic de COVID-19 a été réalisé par RT-PCR après prélèvement nasopharyngé.

Résultats

Au cours de cette période, 30,4 % (1735/5704) des PS ont bénéficié de 3057 écouvillons nasaux. Parmi ceux-ci, 8,0 % (138/1735) étaient infectés par le SRAS-CoV-2. Parmi les PS positifs au SARS-CoV-2, 21,7 % étaient asymptomatiques. Dans les unités COVID et les unités non COVID, le nombre de personnes infectées par le SARS-CoV-2 était respectivement de 5,8 % (13/223) et 8,2 % (125/1512) (p = 0,2). Parmi les PS travaillant hors des unités COVID, 6,4 % (12/188) des agents des unités pédiatriques et 8,1 % (126/1547) des agents des unités adultes ou des laboratoires étaient positifs au SARS-CoV-2 (p = 0,4). Parmi les PS des unités adultes, 6,4 % (8/125) provenaient de la médecine interne, 5,6 % (7/125) de la neurologie, 5,6 % (7/125) de la pharmacie et 5,6 % (7/125) du service médical d’urgence. Parmi les personnes atteintes du SARS-CoV2, les infirmières, les internes/médecins et les aides-soignants étaient les catégories professionnelles les plus touchées avec respectivement 30,0 % (40/138), 21,0 % (29/138) et 10,9 % (15/138). Parmi les médecins, la majorité étaient des internes (70,0 % ; 20/29). Les travailleurs de plus de 50 ans étaient moins susceptibles d’être positifs au SARS-CoV-2 (3,8 % ; 14/373) que les autres travailleurs plus jeunes (9,1 % ; 124/1362) (p < 0,001). Aucun cas grave de COVID-19 n’a été signalé dans notre population au cours de cette période.

Conclusion

Parmi les PS positifs détectés, 21,7 % (25/115) étaient asymptomatiques. Ces données soulignent l’importance du dépistage systématique des cas contacts même asymptomatiques et de l’utilisation d’équipements de protection individuelle (EPI) pour éviter la transmission. Le pourcentage des cas positifs diminuait à mesure que l’âge augmentait, en particulier après l’âge de 45 ans. Les personnels de plus de 45 ans, étant plus expérimentées et se sentant plus à risque, ont pu être mieux protégées ou affectées à des services moins à risque ou confinés à domicile. Les PS travaillant dans des unités COVID-19 n’étaient pas plus souvent infectés que ceux travaillant dans des unités non COVID-19, probablement parce qu’ils étaient plus conscients des dangers et des risques associés au SARS-CoV-2, qu’ils disposaient de plus d’équipements de protection individuelle, qu’ils les portaient de manière plus stricte et qu’ils étaient mieux informés et formés.

Thirteen-week nose-only inhalation exposures of propylene glycol aerosols in Sprague Dawley rats with a lung systems toxicology analysis

The objectives of this study were to increase PG exposure above concentrations tested by Suber et al. and use systems toxicology analysis of lung tissue to understand molecular events. Sprague Dawley rats were exposed to filtered air (sham), propylene glycol/water (PG/W; 90:10) or a propylene glycol/vegetable glycerin/water (PG/VG/W; 50:40:10) reference. The reference group was added at the high dose to observe any changes that might be associated with a carrier more in line with e-vapor products. Macroscopic examinations and terminal organ weights revealed no observations associated with exposure to PG/W or reference. Food consumption and body weights were unaffected by PG/W or reference when compared to sham. No exposure related alterations were observed in serum chemistry, hematology, coagulation, urinalysis or BALF cytology and clinical chemistry. Although clinical observations of dried red material around the nose in the high dose PG/W group were reported, histopathology showed no nasal hemorrhaging which was previously reported by Suber et al. Non-adverse PG/W and reference related findings of minimal mucous cell hyperplasia were noted in nasal cavity section II. No other exposure-related findings were noted in the primary or recovery necropsies. A systems toxicology analysis on lung tissue showed no statistically significant differentially expressed transcripts or proteins compared to the sham group. The endpoints measured from the PG/W high dose group did not differ significantly from those in the more common carrier PG/VG/W. As anticipated, exposure to PG aerosols was slightly irritating but well tolerated. Accordingly, the highest PG exposure (5 mg/L, 6 hrs/day) was regarded as the NOAEC, corresponding to a PG delivered dose of 1,152 mg/kg/day in rats.

Insight into the role of copper in the promoted photocatalytic removal of NO using Zn2-xCuxCr-CO3 layered double hydroxide

In this work the ability of Zn_2-xCu_xCr-CO₃ layered double hydroxides (LDHs) as highly efficient DeNOx photocatalysts was studied. LDHs with x = 0, 0.2 and 0.4 were prepared using a coprecipitation method. The samples were characterized by different techniques such as XRD, XPS, FT-IR, ICP-MS, TG, SBET, SEM and Diffuse reflectance (DR). The increased amount of copper ions in the LDH layers gave rise to slight changes in the structure and morphology and an important variation of the optical properties of the LDHs. The prepared ZnCuCr-CO₃ photocatalysts exhibited favourable conversion efficiency (51%) and an extraordinary selectivity (97%) for the photochemical NO abatement. The photochemical mechanism was elucidated from DOS, EPR, Femtosecond transient absorption and in-situ DRIFTS studies. The results suggested that the presence of Cu²⁺ ions in the LDH framework introduced new states in the valence band states, thus favouring the production and mobility of e^-/h⁺ charge carriers and a greater production of ⋅O₂^- and ⋅OH.

Should We Worry About Nutrition Of Adults With Minor Burns? An Audit Of Their Intakes

Small burn injuries are managed in an outpatient setting by surgeons and/or nurses. Nutrition in minor burn patients is rarely investigated. This observational study aimed to quantify their nutritional intakes, and o compare them to theoretical adequate values. Their average daily food intakes since injury were evaluated by a dietician using a ten-point visual assessment of consumed portions during the last meal (SEFI tool) and a food anamnesis. Macro- and micronutrient intakes were compared to national recommended dietary allowances (RDA) for healthy subjects: intakes <66% RDA were considered inadequate. Forty-two patients with a median age of 45 (34-56) years, BMI of 25.9 (23.5-28.9) kg/m2, and burn surface area (BSA) of 2 (1-3) % were included. Energy and protein RDA were reached in 28.6 and 71.4% of the patients, respectively. Intakes of n-3 fatty acids were inadequate in 80.9% of the patients. A SEFI <7 was associated with insufficient intakes regards both energy and proteins. Inadequate intakes of different micronutrients were frequently observed, but no risk factors could be detected. Vitamin A and C were the most impacted: 71.4% of the patients had inadequate intakes. Vitamin D intake was low: 225 (56-431) UI/d. In contrast, intakes of iron, selenium and zinc were adequate in at least 61.9% of the patients. In conclusion, this audit highlighted that a majority of macronutrient and micronutrient intakes did not reach the levels recommended by the RDA. Such data should help in designing further studies aimed at assessing the impact of optimized nutrition on outcomes.

RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT

RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).

Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition

During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.

Secondary structure of the SARS-CoV-2 5'-UTR

The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.

Impact of the method chosen for the analysis of recurrences after radiotherapy for head and neck cancers: volume-based, point-based and combined methods

Intensity modulated radiation therapy for head and neck is a complex technique. Inappropriate delineation and/or dose distribution can lead to recurrences. Analysis of these recurrences should lead to improve clinical practice. For several years, different methods of analysis have been described. The purpose of this review is to describe these different methods and to discuss their advantages and limitations. The first published methods used a volume-based approach studying the entire volume of recurrence according to initial target volumes, or dose distribution. The main limitation of these methods was that the volume of recurrence studied was dependent on the delay in diagnosis of that recurrence. Subsequently, other methods used point-based approaches, conceptualizing recurrence either as a spherical expansion from a core of radioresistant cells (center of mass of recurrence volume) or using a more clinical approach, taking into account tumor expansion pathways. More recently, more precise combined methods have been described, combining the different approaches. The choice of method is decisive for conclusions on the origin of recurrence.

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host.IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

The VINON-LOCA test facility: exploring the LOCA phenomenology through an out-of-pile thermal sequence on irradiated pressurized fuel rod

Since the out-of-pile semi-integral tests performed at Studsvik in 2011 for the NRC [1] and the Halden Loss-Of-Coolant Accident (LOCA) test series IFA-650 [2], a major safety interest has raised for Fuel Fragmentation, Relocation and Dispersal (FFRD) during a LOCA sequence. In addition to the characteristics of the fuel ejected from the rod after the clad failure, the fuel behaviour before the clad failure is still to be investigated, especially its fragmentation and its possible relocation within the rod during the clad ballooning phase. Furthermore, the chronology and the sequencing of these phenomena is of particular interest.

For this purpose, the VINON-LOCA program, lying in the framework of a trilateral agreement between EDF, Framatome and CEA, is aimed at performing Out-Of-Pile heating tests on irradiated repressurized fuel rods, reproducing a typical Loss Of Coolant Accident thermal sequence. The VINON-LOCA experimental set-up is located in the so-called VERDON lab of the LECA-STAR hot cell complex. This lab was dedicated to the VERDON-ISTP program [3]. The VINON-LOCA set-up is thus largely instrumented for addressing not only these FFRD topics, but also Fission Gas Release (FGR), combining both online measurement (gamma stations, gamma camera, acoustic sensor, pressure, temperatures, flow meters, microGC…), and preand post-test characterization (gamma scanning, tomography, metrology, fuel fragments weighing and sieving, gas analyses…).

An extensive and substantial qualification campaign has been performed to validate the furnace design regarding the desired test conditions, and to qualify the instrumentation. Following some preliminary modelling and calculations, it has included tests on an out-of-cell twin mockup and tests on dummy inactive rods in the hot cell. This allowed achieving successfully the first experimental qualification test of the program end of 2019 on an irradiated UO2 fuel rodlet. A second irradiated experiment is planned with increased instrumentation capabilities, notably a 2D gamma camera for online fuel motion detection.

eIF3 interacts with histone H4 messenger RNA to regulate its translation

In eukaryotes, various alternative translation initiation mechanisms have been unveiled for the translation of specific mRNAs. Some do not conform to the conventional scanning-initiation model. Translation initiation of histone H4 mRNA combines both canonical (cap-dependent) and viral initiation strategies (no-scanning, internal recruitment of initiation factors). Specific H4 mRNA structures tether the translation machinery directly onto the initiation codon and allow massive production of histone H4 during the S phase of the cell cycle. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), was shown to selectively recruit and control the expression of several cellular mRNAs. Whether eIF3 mediates H4 mRNA translation remains to be elucidated. Here, we report that eIF3 binds to a stem-loop structure (eIF3-BS) located in the coding region of H4 mRNA. Combining cross-linking and ribonucleoprotein immunoprecipitation experiments in vivo and in vitro, we also found that eIF3 binds to H1, H2A, H2B, and H3 histone mRNAs. We identified direct contacts between eIF3c, d, e, g subunits, and histone mRNAs but observed distinct interaction patterns to each histone mRNA. Our results show that eIF3 depletion in vivo reduces histone mRNA binding and modulates histone neosynthesis, suggesting that synthesis of histones is sensitive to the levels of eIF3. Thus, we provide evidence that eIF3 acts as a regulator of histone translation.

The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation

SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.

How Many Messenger RNAs Can Be Translated by the START Mechanism?

Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. “Structure Assisted RNA Translation”, or “START”, has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6–2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6–4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2–2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life.

Identification of 6-amino-1H-pyrazolo[3,4-d]pyrimidines with in vivo efficacy against visceral leishmaniasis

The development of a chemical series with oral efficacy against visceral leishmaniasis is described.

Visceral leishmaniasis (VL) affects millions of people across the world, largely in developing nations. It is fatal if left untreated and the current treatments are inadequate. As such, there is an urgent need for new, improved medicines. In this paper, we describe the identification of a 6-amino-N-(piperidin-4-yl)-1H-pyrazolo[3,4-d]pyrimidine scaffold and its optimization to give compounds which showed efficacy when orally dosed in a mouse model of VL.

The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity

Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.

Crowdsourcing: A novel tool to elicit the student voice in the curriculum design process for an undergraduate diagnostic radiography degree programme

INTRODUCTION

Stakeholder participation in healthcare curriculum design is an important aspect of higher education with stakeholders including students, staff members, clinical partners, healthcare organisations, patients and members of the public. Significantly, student co-creation, of the curriculum, has become increasingly important. Yet there is limited research which addresses how to engage this group in design processes.

METHODS

This paper represents the first phase of a three stage action research spiral whereby the authors evaluated the use of a novel tool for curriculum design processes, anonymised crowdsourcing. This initial phase was open to all students enrolled on an undergraduate diagnostic radiography programme in the UK. To confirm the reliability of the crowdsource design an established eight point crowdsourcing verification tool was applied.

RESULTS

Twenty-three unique ideas were generated by participants, 40 comments made and 173 votes cast. Inductive analysis of the comments generated five themes. These included: the role of technology enhanced learning; simulation activities; patient focused curriculum; mental wealth (resilience) authentic assessment approaches. An evaluation of those who had and had not engaged highlighted areas of improvement for the administration of the second and third iterations which will include a wider pool of participants.

CONCLUSION

This study from a single programme offers lessons for others wishing to adopt and develop this approach elsewhere.

IMPLICATIONS FOR PRACTICE

Several ideas elicited by the crowdsource have been considered by the curriculum design team and will be implemented in the 2020 curriculum thus demonstrating the impact on local education practice of this research approach.

Natural History of Perianal Fistulising Lesions in Patients With Elderly-onset Crohn's Disease: A Population-based Study

INTRODUCTION

Most studies of elderly-onset Crohn's disease [CD; diagnosed in patients aged 60 or over] have described a mild course. However, data on the natural history of perianal fistulising CD [pfCD] in this population are scarce. In a population-based cohort study, we described the prevalence, natural history, and treatment of pfCD in patients with elderly-onset CD vs patients with paediatric-onset CD.

METHOD

All patients diagnosed with CD at or after the age of 60 between 1988 and 2006, were included [n = 372]. Logistic regression, Cox models, and a nested case-control method were used to identify factors associated with pfCD.

RESULTS

A total of 34 elderly patients [9% of the 372] had pfCD at diagnosis. After a median follow-up of 6 years (interquartile range [IQR]: 3; 10), 59 patients [16%] had pfCD; the same prevalence [16%] was observed in paediatric-onset patients. At last follow-up, anal incontinence was more frequent in elderly patients with pfCD than in elderly patients without pfCD [22% vs 4%, respectively; p < 10-4]. Rectal CD at diagnosis was associated with pfCD: hazard ratio (95% confidence interval [CI] = 2.8 [1.6-5.0]). Although 37% of the patients received immunosuppressants and 17% received anti-tumour necrosis factor agents, 24% [14 out of 59] had a definitive stoma at last follow-up.

CONCLUSION

During the first 6 years of disease, the prevalence of pfCD was similar in elderly and paediatric patients. Rectal involvement was associated with the appearance of pfCD in elderly-onset patients. Around a quarter of patients with elderly-onset CD will have a stoma. Our results suggest that treatment with biologics should be evaluated in these patients.

Moving Towards Common Data Elements and Core Outcome Measures in Frailty Research

With aging populations around the world, frailty is becoming more prevalent increasing the need for health systems and social systems to deliver optimal evidence based care. However, in spite of the growing number of frailty publications, high-quality evidence for decision making is often lacking. Inadequate descriptions of the populations enrolled including frailty severity and frailty conceptualization, lack of use of validated frailty assessment tools, utilization of different frailty instruments between studies, and variation in reported outcomes impairs the ability to interpret, generalize and implement the research findings. The utilization of common data elements (CDEs) and core outcome measures (COMs) in clinical trials is increasingly being adopted to address such concerns. To catalyze the development and use of CDEs and COMs for future frailty studies, the Canadian Frailty Network (www.cfn-nce.ca; CFN), a not-for-profit pan-Canadian nationally-funded research network, convened an international group of experts to examine the issue and plan the path forward. The meeting was structured to allow for an examination of current frailty evidence, ability to learn from other COMs and CDEs initiatives, discussions about specific considerations for frailty COMs and CDEs and finally the identification of the necessary steps for a COMs and CDEs consensus initiative going forward. It was agreed at the onset of the meeting that a statement based on the meeting would be published and herein we report the statement.

Use of short-lived positron emitters for in-beam and real-time β+ range monitoring in proton therapy

AIM

The purpose of this work is to evaluate the precision with which the GEANT4 toolkit simulates the production of β⁺ emitters relevant for in-beam and real-time PET in proton therapy.

BACKGROUND

An important evolution in proton therapy is the implementation of in-beam and real-time verification of the range of protons by measuring the correlation between the activity of β⁺ and dose deposition. For that purpose, it is important that the simulation of the various β⁺ emitters be sufficiently realistic, in particular for the ¹²N short-lived emitter that is required for efficient in-beam and real-time monitoring.

METHODS

The GEANT4 toolkit was used to simulate positron emitter production for a proton beam of 55 MeV in a cubic PMMA target and results are compared to experimental data.

RESULTS

The three β⁺ emitters with the highest production rates in the experimental data (¹¹C, ¹⁵O and ¹²N) are also those with the highest production rate in the simulation. Production rates differ by 8% to 174%. For the ¹²N isotope, the β⁺ spatial distribution in the simulation shows major deviations from the data. The effect of the long range (of the order of 20 mm) of the β⁺ originating from ¹²N is also shown and discussed.

CONCLUSIONS

At first order, the GEANT4 simulation of the β⁺ activity presents significant deviations from the data. The need for precise cross-section measurements versus energy below 30 MeV is of first priority in order to evaluate the feasibility of in-beam and real-time PET.

Bridging inhaled aerosol dosimetry to physiologically based pharmacokinetic modeling for toxicological assessment: nicotine delivery systems and beyond

One of the challenges for toxicological assessment of inhaled aerosols is to accurately predict their deposited and absorbed dose. Transport, evolution, and deposition of liquid aerosols are driven by complex processes dominated by convection-diffusion that depend on various factors related to physics and chemistry. These factors include the physicochemical properties of the pure substance of interest and associated mixtures, the physical and chemical properties of the aerosols generated, the interplay between different factors during transportation and deposition, and the subject-specific inhalation topography. Several inhalation-based physiologically based pharmacokinetic (PBPK) models have been developed, but the applicability of these models for aerosols has yet to be verified. Nicotine is among several substances that are often delivered via the pulmonary route, with varied kinetics depending upon the route of exposure. This was used as an opportunity to review and discuss the current knowledge and state-of-the-art tools combining aerosol dosimetry predictions with PBPK modeling efforts. A validated tool could then be used to perform for toxicological assessment of other inhaled therapeutic substances. The Science Panel from the Alliance of Risk Assessment have convened at the "Beyond Science and Decisions: From Problem Formulation to Dose-Response Assessment" workshop to evaluate modeling approaches and address derivation of exposure-internal dose estimations for inhaled aerosols containing nicotine or other substances. The discussion involved PBPK model evaluation criteria, challenges, and choices that arise in such a model design, development, and application as a computational tool for use in human toxicological assessments.

In-beam tests of a PET demonstrator (LAPD) for hadrontherapy beam ballistic control: data comparison to Geant4 Monte-Carlo predictions

This paper describes a small prototype of an in beam PET like detector, named ”Large Acceptance Pixelized Detector” (LAPD), developed to test technical concepts for the ion range control in the context of cancer treatments using proton or ion beams. The mechanical characteristics of this detector together with the read-out electronics are first presented. Then, results of a first experiment, performed on a 65 MeV proton beamline, are reported. Finally, we discuss the ability of Geant4 Monte-Carlo to reproduce the experimental data.

Five-year survival and prognostic factors according to histology in 6101 non-small-cell lung cancer patients

OBJECTIVE

To estimate five-year survival in non-small-cell lung cancer (NSCLC) patients according to histology and to identify independent prognostic factors by histology.

METHODS

Data were obtained during the KBP-2010-CPHG study, which included all new cases of primary lung cancer diagnosed in 2010 in 104 non-academic hospitals.

RESULTS

In all, 3199 patients had adenocarcinoma (ADC), 1852 squamous cell carcinoma (SCC), 754 large cell carcinoma (LCC). Five-year survival was 13.3% [12.1%-14.5%] for ADC, 14.3% [12.7%-16.0%] for SCC, 9.6% [7.6%-11.9%] for LCC (P<0.001). Performance status, weight loss prior to diagnosis and tumour stage were consistently significant independent prognostic factors. Age (>70 years; P=0.004), male gender (P<0.001), and smoking (P<0.001) were independent negative prognostic factors for ADC. Epidermal Growth Factor Receptor (EGFR)-mutation tests, performed in 1638 ADC patients, were positive for 186. Five-year survival was 14.7% [10.3%-21%] and 10.9% [9.4%-12.6%] for mutated and wild-type EGFR, respectively (P<0.001). EFGR mutation was an independent positive prognostic factor (HR=0.5 [0.4-0.6], P<0.001); however, the proportional hazards assumption was not fulfilled and hazards were inverted after 35 months.

CONCLUSIONS

Five-year survival in patients managed in French non-academic hospitals for primary NSCLC in 2010 remained poor (<15%), whatever the histologic type. The independent negative prognostic factors for five-year survival were: weight, particularly weight loss prior to diagnosis; smoking (active or former) at diagnosis in ADC and LCC and smoking level at diagnosis in smoker patients with SCC. The independent positive prognostic factors were young age and female gender for ADC.

[Tolerance of hypofractionated stereotactic radiotherapy for hepatic tumours]

PURPOSE

The purpose of the study was to evaluate the outcomes of stereotactic radiation therapy for primary and secondary liver tumours in Jean-Perrin cancer centre (Clermont-Ferrand, France) in terms of efficacy and safety.

MATERIALS AND METHODS

Between December 2013 and June 2016, 25 patients were included. Treatment was performed on a linear accelerator Novalis TX^®. The prescription dose was 42 to 60Gy in three to five fractions. Local control at 1 year was evaluated with modified Response Evaluation Criteria in Solid Tumours (mRECIST) and RECIST criteria. Acute and late toxicity were evaluated with Common Terminology Criteria for Adverse Events (CTCAE) v4.0 criteria.

RESULTS

Median follow-up was 10.5 months. Treatment tolerance was good with few side effects grade 3 or above, no acute toxicity and only one late toxicity. We have highlighted that hepatic artery haemorrhage was associated with the presence of a biliary prosthesis in contact with the artery (P=0.006) and in the irradiation field. There was no correlation with the dose delivered to the artery and hepatic artery haemorrhage.

CONCLUSION

Stereotactic radiation therapy for liver tumours allows a good local control with few secondary effects. Caution should be exercised when treating patients with biliary prostheses in the vicinity of the target volume because there is a risk of haemorrhage of the hepatic artery in contact with the prosthesis.

A variant in MRPS14 (uS14m) causes perinatal hypertrophic cardiomyopathy with neonatal lactic acidosis, growth retardation, dysmorphic features and neurological involvement

Dysfunction of mitochondrial translation is an increasingly important molecular cause of human disease, but structural defects of mitochondrial ribosomal subunits are rare. We used next-generation sequencing to identify a homozygous variant in the mitochondrial small ribosomal protein 14 (MRPS14, uS14m) in a patient manifesting with perinatal hypertrophic cardiomyopathy, growth retardation, muscle hypotonia, elevated lactate, dysmorphy and mental retardation. In skeletal muscle and fibroblasts from the patient, there was biochemical deficiency in complex IV of the respiratory chain. In fibroblasts, mitochondrial translation was impaired, and ectopic expression of a wild-type MRPS14 cDNA functionally complemented this defect. Surprisingly, the mutant uS14m was stable and did not affect assembly of the small ribosomal subunit. Instead, structural modeling of the uS14m mutation predicted a disruption to the ribosomal mRNA channel.Collectively, our data demonstrate pathogenic mutations in MRPS14 can manifest as a perinatal-onset mitochondrial hypertrophic cardiomyopathy with a novel molecular pathogenic mechanism that impairs the function of mitochondrial ribosomes during translation elongation or mitochondrial mRNA recruitment rather than assembly.