The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This Portal has been coupled with other resources like Viral AI and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this Portal, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis.

Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.

Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development.

The jasmonic acid (JA) signalling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis. The Laccaria bicolor effector MiSSP7 stabilizes JA corepressor JAZ6, thereby inhibiting the activity of Populus MYC2 transcription factors. Although the role of MYC2 in orchestrating plant defences against pathogens is well established, its exact contribution to ECM symbiosis remains unclear. This information is crucial for understanding the balance between plant immunity and symbiotic relationships. Transgenic poplars overexpressing or silencing for the two paralogues of MYC2 transcription factor (MYC2s) were produced, and their ability to establish ectomycorrhiza was assessed. Transcriptomics and DNA affinity purification sequencing were performed. MYC2s overexpression led to a decrease in fungal colonization, whereas its silencing increased it. The enrichment of terpene synthase genes in the MYC2-regulated gene set suggests a complex interplay between the host monoterpenes and fungal growth. Several root monoterpenes have been identified as inhibitors of fungal growth and ECM symbiosis. Our results highlight the significance of poplar MYC2s and terpenes in mutualistic symbiosis by controlling root fungal colonization. We identified poplar genes which direct or indirect control by MYC2 is required for ECM establishment. These findings deepen our understanding of the molecular mechanisms underlying ECM symbiosis.

SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice.

The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution.

Relationship between prehospital clinical status intracranial pressure and outcomes in pediatric patients with severe head trauma

Introduction: The prehospital phase of the management of pediatric severe traumatic brain injury may have a direct influence on the results. Objective: To evaluate the influence of prehospital variables on intracranial pressure and the results in pediatric patients with severe TBI. Method: A descriptive study of 41 pediatric patients who were admitted to the medical emergency department and later admitted to the pediatric intensive care unit due to severe head trauma was carried out between January 2003 and December 2018. Results: children aged 5-17 years predominate, and the highest number of cases were received between 0-3h at the neurotrauma center. Of the 41 cases, 27 arrived with a non-expedited airway and hypoxia was verified upon arrival by pulse oximetry. A correlation was observed between arterial hypotension on admission and elevated intracranial pressure in 9 of 15 children (60%) and in the deceased (40%). Discussion: Clinical conditions, oxygenation, arterial hypotension, and treatment in the prehospital phase may influence the state of intracranial pressure and other intracranial variables in pediatric patients with severe head injury.

Introducción: La fase prehospitalaria del manejo del traumatismo craneoencefálico grave pediátrico puede tener una influencia directa en los resultados. Objetivo: Evaluar la influencia de variables prehospitalarias sobre la presión intracraneal y los resultados en pacientes pediátricos con TCE grave. Metodología: Se realizó un estudio descriptivo de 41 pacientes pediátricos que ingresaron al servicio de urgencias médicas y posteriormente ingresaron a la unidad de cuidados intensivos pediátricos por traumatismo craneoencefálico severo entre enero de 2003 y diciembre de 2018. Resultados: predominan los niños de 5 a 17 años, y el mayor número de casos se recibieron entre las 0-3h en el centro de neurotrauma. De los 41 casos, 27 llegaron con vía aérea no acelerada y se verificó hipoxia al llegar mediante oximetría de pulso. Se observó correlación entre hipotensión arterial al ingreso y presión intracraneal elevada en 9 de 15 niños (60%) y en los fallecidos (40%). Discusión: Las condiciones clínicas, la oxigenación, la hipotensión arterial y el tratamiento en la fase prehospitalaria pueden influir en el estado de la presión intracraneal y otras variables intracraneales en pacientes pediátricos con traumatismo craneoencefálico grave.

Influence of the Magnetic Tip on Heterodimers in Electron Spin Resonance Combined with Scanning Tunneling Microscopy.

Investigating the quantum properties of individual spins adsorbed on surfaces by electron spin resonance combined with scanning tunneling microscopy (ESR-STM) has shown great potential for the development of quantum information technology on the atomic scale. A magnetic tip exhibiting high spin polarization is critical for performing an ESR-STM experiment. While the tip has been conventionally treated as providing a static magnetic field in ESR-STM, it was found that the tip can exhibit bistability, influencing ESR spectra. Ideally, the ESR splitting caused by the magnetic interaction between two spins on a surface should be independent of the tip. However, we found that the measured ESR splitting of a metal atom-molecule heterodimer can be tip-dependent. Detailed theoretical analysis reveals that this tip-dependent ESR splitting is caused by a different interaction energy between the tip and each spin of the heterodimer. Our work provides a comprehensive reference for characterizing tip features in ESR-STM experiments and highlights the importance of employing a proper physical model when describing the ESR tip, in particular, for heterospin systems.

Electric-Field-Driven Spin Resonance by On-Surface Exchange Coupling to a Single-Atom Magnet.

Coherent control of individual atomic and molecular spins on surfaces has recently been demonstrated by using electron spin resonance (ESR) in a scanning tunneling microscope (STM). Here, a combined experimental and modeling study of the ESR of a single hydrogenated Ti atom that is exchange-coupled to a Fe adatom positioned 0.6-0.8 nm away by means of atom manipulation is presented. Continuous wave and pulsed ESR of the Ti spin show a Rabi rate with two contributions, one from the tip and the other from the Fe, whose spin interactions with Ti are modulated by the radio-frequency electric field. The Fe contribution is comparable to the tip, as revealed by its dominance when the tip is retracted, and tunable using a vector magnetic field. The new ESR scheme allows on-surface individual spins to be addressed and coherently controlled without the need for magnetic interaction with a tip. This study establishes a feasible implementation of spin-based multi-qubit systems on surfaces.

Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse.

Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on autosomal DNA methylation patterns and its contribution to sex bias in methylation, we identified Y chromosome dependent differentially methylated regions (yDMRs) using whole-genome bisulfite sequencing methylation data from livers of mice with different combinations of sex-chromosome complement and gonadal sex. Nearly 90% of the autosomal yDMRs mapped to transposable elements (TEs) and most of them had lower methylation in XY compared to XX or XO mice. Follow-up analyses of four reporter autosomal yDMRs showed that Y-dependent methylation levels were consistent across most somatic tissues but varied in strains with different origins of the Y chromosome, suggesting that genetic variation in the Y chromosome influenced methylation levels of autosomal regions. Mice lacking the q-arm of the Y chromosome (B6.NPYq-2) as well as mice with a loss-of-function mutation in Kdm5d showed no differences in methylation levels compared to wild type mice. In conclusion, the Y-linked modifier of TE methylation is likely to reside on the short arm of Y chromosome and further studies are required to identify this gene.

More than a 'Hundred Days War': Persistent SARS-CoV-2 infection in a patient with ANCA-associated vasculitis.

BACKGROUND: Few reports exist on the characteristics and outcomes of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in immunocompromised hosts. METHODS: A 49-year-old patient with granulomatosis with polyangiitis (GPA) and a renal transplant experienced multiple hospitalizations for coronavirus disease 2019 (COVID-19) pneumonia and relapses between October 2020 and February 2021. Careful chart review of medical history, hospitalizations, and microbiological testing including SARS-CoV-2 cycle threshold values, therapies, and imaging was undertaken. SARS-CoV-2 genome sequencing was performed in five viral samples to distinguish persistent infection from re-infection with a different strain. RESULTS: Sequencing confirmed that all samples tested were from the same viral lineage, indicating a long-term, persistent infection rather than re-infection with a new strain. The patient ultimately stabilized after two courses of remdesivir plus dexamethasone, replacement intravenous immunoglobulin, and bamlanivimab. Rituximab maintenance therapy for vasculitis remains on hold. CONCLUSIONS: SARS-CoV-2 may persist for several months in immunocompromised hosts and may go unrecognized as an ongoing active infection. More studies are needed to determine how to optimize COVID-19 treatment in this vulnerable population.

HISTORIQUE: Il existe peu de rapports sur les caractéristiques et les issues de l'infection par le coronavirus 2 du syndrome respiratoire aigu sévère (SRAS-CoV-2) chez les hôtes immunodéprimés. MÉTHODOLOGIE: UNE PATIENTE de 49 ans receveuse d'une transplantation rénale atteinte d'une granulomatose avec polyangéite a été hospitalisée à de multiples reprises à cause d'une pneumonie à maladie à coronavirus 2019 (COVID-19) et de récidives entre octobre 2020 et février 2021. Les chercheurs ont exécuté une analyse attentive du dossier pour connaître l'histoire médicale de la patiente, les hospitalisations et les tests microbiologiques effectués, y compris les valeurs seuils du cycle du SRAS-CoV-2, les traitements et les techniques d'imagerie. Ils ont procédé au séquençage du génome du SRAS-CoV-2 dans cinq prélèvements viraux pour distinguer l'infection persistante de la réinfection par une souche différente. RÉSULTATS : Le séquençage a confirmé que tous les prélèvements effectués provenaient de la même lignée virale, ce qui détermine une infection persistante prolongée plutôt qu'une réinfection par une nouvelle souche. L'état de la patiente a fini par se stabiliser après deux traitements au remdésivir combiné à de la dexaméthasone, une thérapie de substitution par immunoglobuline intraveineuse et du bamlanivimab. Un traitement d'entretien de la vasculite au rituximab demeure en suspens. CONCLUSIONS: Le SRAS-CoV-2 peut persister plusieurs mois chez les hôtes immunodéprimés, et un état d'infection active continue peut passer inaperçu. Plus d'études devront être réalisées pour déterminer le moyen d'optimiser le traitement de la COVID-19 dans cette population vulnérable.

Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase.

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔGb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.

Synthesis, resolution, and absolute configuration determination of a vicinal amino alcohol with axial chirality. Application to the synthesis of new box and pybox ligands.

New racemic vicinal amino alcohol derivatives with 4-benzylidenecyclohexane skeleton and axial chirality have been prepared. A preparatively easy and efficient protocol for resolution of the N-benzoylamino alcohol is described. Using a 250 × 20 mm (L × ID) Chiralpak® IA column, and the appropriate mixture of n-hexane/ethanol/chloroform as eluent, both enantiomers of N-benzoylamino alcohol 3 are obtained with >99% enantiomeric excess (ee) by successive injections of a solution of the racemic sample in chloroform. The obtained axially chiral vicinal amino alcohol is used to synthesize structurally novel bisoxazoline ligands in high yields.

Design, synthesis and structure-activity evaluation of novel 2-pyridone-based inhibitors of α-synuclein aggregation with potentially improved BBB permeability.

The treatment of Parkinson's disease (PD), the second most common neurodegenerative human disorder, continues to be symptomatic. Development of drugs able to stop or at least slowdown PD progression would benefit several million people worldwide. SynuClean-D is a low molecular weight 2-pyridone-based promising drug candidate that inhibits the aggregation of α-synuclein in human cultured cells and prevents degeneration of dopaminergic neurons in a Caenorhabditis elegans model of PD. Improving SynuClean-D pharmacokinetic/pharmacodynamic properties, performing structure/activity studies and testing its efficacy in mammalian models of PD requires the use of gr-amounts of the compound. However, not enough compound is on sale, and no synthetic route has been reported until now, which hampers the molecule progress towards clinical trials. To circumvent those problems, we describe here an efficient and economical route that enables the synthesis of SynuClean-D with good yields as well as the synthesis of SynuClean-D derivatives. Structure-activity comparison of the new compounds with SynuClean-D reveals the functional groups of the molecule that can be disposed of without activity loss and those that are crucial to interfere with α-synuclein aggregation. Several of the derivatives obtained retain the parent's compound excellent in vitro anti-aggregative activity, without compromising its low toxicity. Computational predictions and preliminary testing indicate that the blood brain barrier (BBB) permeability of SynuClean-D is low. Importantly, several of the newly designed and obtained active derivatives are predicted to display good BBB permeability. The synthetic route developed here will facilitate their synthesis for BBB permeability determination and for efficacy testing in mammalian models of PD.

A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada.

BACKGROUND: Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. METHODS: Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. RESULTS: Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and "snowbird" destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7-12 led to the largest transmission lineages of the first wave (accounting for 52-75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. CONCLUSIONS: Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

Selective Targeting of Human and Animal Pathogens of the Helicobacter Genus by Flavodoxin Inhibitors: Efficacy, Synergy, Resistance and Mechanistic Studies.

Antimicrobial resistant (AMR) bacteria constitute a global health concern. Helicobacter pylori is a Gram-negative bacterium that infects about half of the human population and is a major cause of peptic ulcer disease and gastric cancer. Increasing resistance to triple and quadruple H. pylori eradication therapies poses great challenges and urges the development of novel, ideally narrow spectrum, antimicrobials targeting H. pylori. Here, we describe the antimicrobial spectrum of a family of nitrobenzoxadiazol-based antimicrobials initially discovered as inhibitors of flavodoxin: an essential H. pylori protein. Two groups of inhibitors are described. One group is formed by narrow-spectrum compounds, highly specific for H. pylori, but ineffective against enterohepatic Helicobacter species and other Gram-negative or Gram-positive bacteria. The second group includes extended-spectrum antimicrobials additionally targeting Gram-positive bacteria, the Gram-negative Campylobacter jejuni, and most Helicobacter species, but not affecting other Gram-negative pathogens. To identify the binding site of the inhibitors in the flavodoxin structure, several H. pylori-flavodoxin variants have been engineered and tested using isothermal titration calorimetry. An initial study of the inhibitors capacity to generate resistances and of their synergism with antimicrobials commonly used in H. pylori eradication therapies is described. The narrow-spectrum inhibitors, which are expected to affect the microbiota less dramatically than current antimicrobial drugs, offer an opportunity to develop new and specific H. pylori eradication combinations to deal with AMR in H. pylori. On the other hand, the extended-spectrum inhibitors constitute a new family of promising antimicrobials, with a potential use against AMR Gram-positive bacterial pathogens.

Dependencia funcional en pacientes adultos mayores con diabetes mellitus tipo 2 en Lima, Perú / Functional Dependence in Older Adults Patients with Type 2 Diabetes Mellitus in Lima, Peru

RESUMEN Fundamento: la dependencia funcional contempla la presencia de limitaciones en las actividades diarias y está relacionada con la disminución de todas las capacidades y la interacción con el entorno. Este factor está relacionado con diferentes comorbilidades que se presentan en los adultos mayores. Una de estas comorbilidaes es la diabetes mellitus. Objetivo: determinar la prevalencia de dependencia funcional en pacientes adultos mayores con diagnóstico de diabetes mellitus tipo 2 en la clínica de día y consultorio externo del Centro Geriátrico Naval en el periodo 2010-2015. Método: se realizó un estudio transversal con análisis secundario de la base de datos Texas-Camena UTMB 2010-2015 del Centro de Investigación del Envejecimiento de la Universidad San Martín de Porres. Se consideró como variable dependiente a la dependecia funcional y las variables independientes fueron las características sociodemográficas y los antecedentes personales y patológicos. Se realizó estadística descriptiva basada en el cálculo de frecuencias, porcentajes, dispersión y medidas de tendencia central. Para encontrar la asociacion entre las variables independientes y la dependencia funcional se utilizó la prueba de Chi cuadrado o la prueba exacta de Fisher. Los cálculos se realizaron con un nivel de confianza de 95 %. Resultados: el promedio de edad fue de 77,5± 8 años. En 9 pacientes (3,3 %) se detectó dependencia total; en 5 (1,9 %) fue severa; en 154 (57,0 %) fue moderada; y en 33 (12,2 %) fue baja. De ellos 69 (25,6 %) no tuvieron dependencia. El rango de edad de 83-100 años fue un factor asociado independiente para presentar dependencia funcional (OR=2,64 IC 95 % [1,071-6,510]). Conclusiones: el 73,4 % de la población en estudio presentó algún nivel de dependencia funcional, siendo el rango de edad de 83-100 años un factor independiente asociado para presentar dependencia funcional.

ABSTRACT Background: functional dependence considers the presence of limitations in daily activities and is related to the decrease in all abilities and interaction with the environment. This factor is related to different comorbidities that occur in older adults. One of these comorbidities is diabetes mellitus. Objective: to determine the prevalence of functional dependence in elderly patients diagnosed with type 2 diabetes mellitus in the day clinic and outpatient clinic of the Naval Geriatric Center in the period 2010-2015. Method: a cross-sectional study was carried out with secondary analysis of the Texas-Camena UTMB 2010-2015 database of the San Martín de Porres University Center for Research on Aging. Functional dependence was considered as a dependent variable and the independent variables were sociodemographic characteristics and personal and pathological antecedents. Descriptive statistics were performed based on the calculation of frequencies, percentages, dispersion and measures of central tendency. To find the association between the independent variables and the functional dependence, the Chi-square test or Fisher's exact test was used. The calculations were made with a confidence level of 95 %. Results: the average age was 77.5 ± 8 years. In 9 patients (3.3 %) total dependence was detected; in 5 (1.9 %) it was severe; in 154 (57.0 %) it was moderate; and in 33 (12.2 %) it was low. Of them 69 (25.6 %) did not have dependency. The age range of 83-100 years old was an independent associated factor for presenting functional dependence (OR = 2.64 95 % CI [1.071-6.510]). Conclusions: the 73.4 % of the study population presented some level of functional dependence, with the age range of 83-100 years old being an independent factor associated with presenting functional dependence.

Asymmetric synthesis of (1R,5S)-2-methyl-6,7-benzomorphan via Aza-Prins reaction.

(1R,5S)-2-Methyl-6,7-benzomorphan has been synthesised from (R)-(benzyloxy)(phenyl)acetaldehyde. On a 2-mmol scale Bi (OTf)3 promoted Aza-Prins reaction with N-tosylhomoallylamine afforded an 88/12 mixture of 6-oxa-2-azabicyclo[3.2.1]octanes. Major diastereoisomer was converted to enantiomerically pure (2S,4S)-2-benzyl-1- methylpiperidin-4-ol via a high-yielding sequence hydrogenolysis/N-detosylation/N-methylation. Acid-catalysed intramolecular Friedel-Crafts cyclisation of the piperidinol afforded (1R,5S)-2-methyl-6,7-benzomorphan in five steps with a yield of 25%.

Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver.

Sexual dimorphism in gene regulation, including DNA methylation, is the main driver of sexual dimorphism in phenotypes. However, the questions of how and when sex shapes DNA methylation remain unresolved. Recently, using mice with different combinations of genetic and phenotypic sex, we identified sex-associated differentially methylated regions (sDMRs) that depended on the sex phenotype. Focusing on a panel of validated sex-phenotype dependent male- and female-biased sDMRs, we tested the developmental dynamics of sex bias in liver methylation and the impacts of mutations in the androgen receptor, estrogen receptor alpha, or the transcriptional repressor Bcl6 gene. True hermaphrodites that carry both unilateral ovaries and contralateral testes were also tested. Our data show that sex bias in methylation either coincides with or follows sex bias in the expression of sDMR-proximal genes, suggesting that sex bias in gene expression may be required for demethylation at certain sDMRs. Global ablation of AR, ESR1, or a liver-specific loss of BCL6, all alter sDMR methylation, whereas presence of both an ovary and a testis delays the establishment of male-type methylation levels in hermaphrodites. Moreover, the Bcl6-LKO shows dissociation between expression and methylation, suggesting a distinct role of BCL6 in demethylation of intragenic sDMRs.

Different patterns in root and soil fungal diversity drive plant productivity of the desert truffle Terfezia claveryi in plantation.

The desert truffle Terfezia claveryi is one of the few mycorrhizal fungi currently in cultivation in semiarid and arid areas. Agroclimatic parameters seem to affect its annual yield, but there is no information on the influence of biotic factors. In this study, fungal diversity was analysed by high-throughput sequencing of the ITS2 rDNA region from soil and root samples to compare productive and non-productive mycorrhizal plants in a 4-years old plantation (Murcia, Spain). The fungal metaprofile was dominated by Ascomycota phylum. Desert truffle productivity was driven by different patterns of fungal species composition in soil (species replacement) and root (species richness differences). Moreover, positive associations for ectomycorrhizal and negative for arbuscular mycorrhizal guilds were found in productive roots, and positive associations for fungal parasite-plant pathogen guild in non-productive ones. Soil samples were dominated by pathotroph and saprotroph trophic modes, showing positive associations for Aureobasidium pullulans and Alternaria sp. in productive areas, and positive associations for Fusarium sp. and Mortierella sp. were found in non-productive soils. Finally, some significant OTUs were identified and associated to ascocarp producing patches, which could serve as predictive and location markers of desert truffle production.

Ultrafast functional profiling of RNA-seq data for nonmodel organisms.

Computational time and cost remain a major bottleneck for RNA-seq data analysis of nonmodel organisms without reference genomes. To address this challenge, we have developed Seq2Fun, a novel, all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. The pipeline starts with raw read quality control: sequencing error correction, removing poly(A) tails, and joining overlapped paired-end reads. It then conducts a DNA-to-protein search by translating each read into all possible amino acid fragments and subsequently identifies possible homologous sequences in a well-curated protein database. Finally, the pipeline generates several informative outputs including gene abundance tables, pathway and species hit tables, an HTML report to visualize the results, and an output of clean reads annotated with mapped genes ready for downstream analysis. Seq2Fun does not have any intermediate steps of file writing and loading, making I/O very efficient. Seq2Fun is written in C++ and can run on a personal computer with a limited number of CPUs and memory. It can process >2,000,000 reads/min and is >120 times faster than conventional workflows based on de novo assembly, while maintaining high accuracy in our various test data sets.