Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network.

Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.

The impact of Covid-19 on demographic components in Spain, 2020-31: A scenario approach.

While considerable attention has been paid to the impact of Covid-19 on mortality and fertility, few studies have attempted to evaluate the pandemic's effect on international migration. We analyse the impact of Covid-19 on births, deaths, and international migration in Spain during 2020, comparing observed data with estimated values assuming there had been no pandemic. We also assess the consequences of three post-pandemic scenarios on the size and structure of the population to 2031. Results show that in 2020, excess mortality equalled 16.2 per cent and births were 6.5 per cent lower than expected. Immigration was the most affected component, at 36.0 per cent lower than expected, while emigration was reduced by 23.8 per cent. If net migration values recover to pre-pandemic levels in 2022, the size and structure of the population in 2031 will be barely affected. Conversely, if levels do not recover until 2025, there will be important changes to Spain's age structure.

Application of the NanoString nCounter System as an Alternative Method to Investigate Molecular Mechanisms Involved in Host Plant Responses to Plasmodiophora brassicae.

Clubroot, caused by the soilborne pathogen Plasmodiophora brassicae, is an important disease of canola (Brassica napus) and other crucifers. The recent application of RNA sequencing (RNA-seq) technologies to study P. brassicae−host interactions has generated large amounts of gene expression data, improving knowledge of the molecular mechanisms of pathogenesis and host resistance. Quantitative PCR (qPCR) analysis has been widely applied to examine the expression of a limited number of genes and to validate the results of RNA-seq studies, but may not be ideal for analyzing larger suites of target genes or increased sample numbers. Moreover, the need for intermediate steps such as cDNA synthesis may introduce variability that could affect the accuracy of the data generated by qPCR. Here, we report the validation of gene expression data from a previous RNA-seq study of clubroot using the NanoString nCounter System, which achieves efficient gene expression quantification in a fast and simple manner. We first confirm the robustness of the NanoString system by comparing the results with those generated by qPCR and RNA-seq and then discuss the importance of some candidate genes for resistance or susceptibility to P. brassicae in the host. The results show that the expression of genes measured using NanoString have a high correlation with the values obtained using the other two technologies, with R > 0.90 and p < 0.01, and the same expression patterns for most genes. The three methods (qPCR, RNA-seq, and NanoString) were also compared in terms of laboratory procedures, time, and cost. We propose that the NanoString nCounter System is a robust, sensitive, highly reproducible, and simple technology for gene expression analysis. NanoString could become a common alternative to qPCR to validate RNA-seq data or to create panels of genes for use as markers of resistance/susceptibility when plants are challenged with different P. brassicae pathotypes.

Rural revival? The rise in internal migration to rural areas during the COVID-19 pandemic. Who moved and Where?

During the outbreak of the COVID-19 pandemic, anecdotal evidence of a "rural revival" emerged mirroring the "urban exodus" hypothesis. Currently, we know that internal migration to rural areas increased in some countries during 2020, although not with the intensity speculated by the media. However, little is known about the attributes of rural areas attracting migrants, demographic composition of migration inflows, and if counterurbanisation movements persisted over 2021. Drawing on administrative population register data, we analysed the main types of rural areas pulling internal migrants in Spain and their demographic characteristics, namely age, sex and place of birth during 2020 and 2020, using the period 2016-2019 as a benchmark. Our results show that in-migration increased in rural areas close to cities and with high prevalence of second homes during 2020, while out-migration declined. Exceptionally high inflows persisted over 2021, but outflows converged to figures observed prior to the pandemic. Inflows to rural areas comprised internal migrants across a wide age spectrum, from young adults and families to retired individuals. These flows also comprised foreign-born, particularly populations of a wide age range from Latin American countries.

Understanding patterns of internal migration during the COVID-19 pandemic in Spain.

Existing empirical work has analysed the impacts of COVID-19 on mortality, fertility and international migration. Less is known about the ways in which the COVID-19 pandemic has influenced the patterns of internal migration. Anecdotal reports of mass migration from large cities to less populated areas have emerged, but lack of data has prevented empirically assessing this hypothesis. Drawing on geographically granular administrative population register data, we aim to analyse the extent of change in the patterns of internal migration across the urban hierarchy in Spain during 2020. Our results show a decline of 2.5% in the number of internal migration moves, particularly during the early stages of the pandemic, returning to pre-pandemic levels in late 2020. Results also reveal unusually large net migration losses in core cities and net migration gains in rural areas. Net migration losses in cities and gains in rural areas particularly accumulated following the elimination of the strict lockdown measures in June. Yet, these net losses and gains trended to pre-pandemic levels in late 2020, and movements between cities, and between cities and suburbs, continued to dominate the internal migration system. Thus, while the COVID-19 pandemic exerted notable changes in the geographic balance of internal migration flows, these changes appear to have been temporary and did not significantly alter the existing structures of the national migration system.

Genetic Structure of Plasmodiophora brassicae Populations Virulent on Clubroot Resistant Canola (Brassica napus).

Clubroot, caused by Plasmodiophora brassicae Woronin, is a significant threat to the canola (Brassica napus L.) industry in Canada. Clubroot resistance has been overcome in more than 200 fields since 2013, representing one of the biggest challenges to sustainable canola production. The genetic structure of 36 single-spore isolates derived from 12 field isolates of P. brassicae collected before and after the introduction of clubroot resistant (CR) canola cultivars (2005-2014) was evaluated by simple sequence repeat (SSR) marker analysis. Polymorphisms were detected in 32 loci with the identification of 93 distinct alleles. A low level of genetic diversity was found among the single-spore isolates. Haploid linkage disequilibrium and number of migrants suggested that recombination and migration were rare or almost absent in the tested P. brassicae population. A relatively clear relationship was found between the genetic structure and virulence phenotypes of the pathogen as defined on the differential hosts of Somé et al., Williams, and the Canadian Clubroot Differential (CCD) set. Although genetic variability within each pathotype group, as classified on each differential system, was low, significant genetic differentiation was observed among the pathotypes. The highest correlation between genetic structure and virulence was found among matrices produced with genetic data and the hosts of the CCD set, with a threshold index of disease of 50% to distinguish susceptible from resistant reactions. Genetically homogeneous single-spore isolates provided a more complete and clearer picture of the population genetic structure of P. brassicae, and the results suggest some promise for the development of pathotype-specific primers.

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae.

Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars 'Wilhelmsburger' (resistant) and 'Laurentian' (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in 'Wilhelmsburger' to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.

[Structured clinical examinations with simulated patients during internal medicine clerkship]. / Descripción y análisis de ECOE con pacientes simulados en internado de Medicina Interna 2016-2017 en Facultad de Medicina Universidad de Chile.

BACKGROUND: Practice is essential in clinical training and can be carried out with simulations. The medical school of the University of Chile performs Objective Structured Clinical Examinations (OSCE) using standardized simulated patients for interns. AIM: To report the experience with OSCE in an environment with a high number of students. MATERIAL AND METHODS: Four hundred sixty-two students, participated in three OSCEs during 2016 and 2017, during their internal medicine clerkship. Each OSCE consisted of five scenarios of ambulatory care patients with prevalent medical conditions. Every student had to perform history taking, physical examination and deliver a diagnostic hypothesis, and a plan for management and counseling. Simulated patients provided feedback. To assess validity and reliability, in an argument-based model, planning and activity development were declared. The results were evaluated according to students' and organization variables, internal consistency, interobserver and theoretical concordance tests. RESULTS: No significant bias was found by demographic features or evaluation moment. Internal consistency was good (Cronbach 0.8). Simulated patient evaluators had a high correlation with medical evaluators (r = 0.7). There was a low correlation between OSCE results and theoretical tests. CONCLUSIONS: OSCE's continuously assess competences during internal medicine clerkship in an environment with a high number of students.

Elimination of hepatitis C virus infection from a hemodialysis unit and impact of treatment on the control of anemia.

INTRODUCTION: In the interferon era, the treatment of hepatitis C virus (HCV) infection in patients on haemodialysis (HD) was limited due to the significant number of treatment-related adverse events (AEs). Direct-acting antivirals (DAAs) have demonstrated their efficacy and safety in the treatment of HCV in patients with advanced chronic kidney disease on haemodialysis. The objective of the study was to evaluate the success in eliminating HCV infection from our dialysis unit using DAAs, and to assess the impact of HCV elimination on clinical and analytical outcomes. PATIENTS AND METHODS: This is a prospective, interventional, single-center study at Hospital Clínic de Barcelona. All HCV-RNA positive patients who received antiviral therapy with DAAs within a 3-year period (2014-2017) were analyzed (n=20). Data on virologic response, adverse events, and biochemical and hematological parameters during and after DAA therapy were analyzed. RESULTS: All patients achieved sustained virologic response (SVR) and only 40% of patients presented with mild AEs. None of the patients presented with HCV reinfection after a 1-year follow-up period, and thus HCV was eliminated from our HD unit. SVR was associated with a significant increase in hemoglobin and hematocrit, and a tendency toward the need for lower doses of iron supplementation with no changes in darbepoetin dose. CONCLUSION: HCV infection can be safely eliminated from HD units with the use of DAAs, preventing new infections in patients and healthcare staff. In the short term, the achievement of SVR is associated with an improvement in the control of anemia.

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

BACKGROUND: Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. RESULTS: Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. CONCLUSIONS: We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.

Exploring the potential association between brominated diphenyl ethers, polychlorinated biphenyls, organochlorine pesticides, perfluorinated compounds, phthalates, and bisphenol A in polycystic ovary syndrome: a case-control study.

BACKGROUND: Polycystic Ovary Syndrome (PCOS) is an endocrine-metabolic disorder that affects approximately 6-10% of women of child-bearing age. Although preliminary studies suggest that certain pollutants may act as endocrine disruptors in animals, little is known about their potential association with PCOS. The objective of this case-control pilot study is to determine whether women with PCOS have higher concentrations of specific environmental contaminants compared to women who have not developed PCOS. METHODS: Fifty-two PCOS case-patients (diagnosed using the National Institutes of Health 1990 definition) and 50 controls were recruited in 2007-2008, from an urban academic medical center in Los Angeles, CA. Brominated diphenyl ethers, polychlorinated biphenyls (PCBs), organochlorine pesticides, and perfluorinated compounds (PFCs) were measured in serum, and phthalates metabolites and bisphenol A (BPA) in urine. RESULTS: PCOS case-patients had significantly higher geometric mean (GM) serum concentrations of two PFCs: perfluorooctanoate (PFOA) (GMcases = 4.1 µg/L, GMcontrols = 2.3 µg/L; p = 0.001) and perfluorooctane sulfonate (PFOS) (GMcases = 8.2 µg/L, GMcontrols = 4.9 µg/L; p = 0.01), and lower urinary concentrations of monobenzyl phthalate (mBzP) (GMcases = 7.5 µg/g creatinine, GMcontrols = 11.7 µg/g creatinine; p = 0.02). Logistic regression, controlling for body mass index, age and race, identified an increased likelihood of PCOS in subjects with higher serum concentrations of PFOA and PFOS (adjusted-ORs = 5.8-6.9, p < 0.05), and with lower urine concentrations of mBzP and mono-n-butyl phthalate (mBP) (aORs = 0.14-0.25, p < 0.05). CONCLUSIONS: Our data suggest that PCOS case-patients may differ from controls in their environmental contaminant profile. PCOS subjects had higher serum concentrations of two PFCs, PFOA and PFOS, and lower urine concentrations of mBP and mBzP. Future studies are needed to confirm these preliminary findings and determine if these chemicals or their precursors may have a role in the pathogenesis of PCOS.

Clubroot-Induced Changes in the Root and Rhizosphere Microbiome of Susceptible and Resistant Canola.

Clubroot is a soilborne disease of canola (Brassica napus) and other crucifers caused by the obligate parasite Plasmodiophora brassicae. In western Canada, clubroot is usually managed by planting-resistant cultivars, but the emergence of resistance-breaking pathotypes of P. brassicae represents a major threat to sustainable canola production. The rhizosphere and root contain beneficial microorganisms that can improve plant health. In this study, we evaluated the effect of two P. brassicae isolates (termed A and B) with different levels of virulence on the root and rhizosphere microbiomes of clubroot-resistant and clubroot-susceptible canola. Additionally, potential biocontrol microorganisms were identified based on taxa antagonistic to clubroot. Although both P. brassicae isolates were classified as pathotype 3A, isolate A caused a higher disease severity index in the resistant canola genotype compared with isolate B. Metabarcoding analysis indicated a shift in the bacterial and fungal communities in response to inoculation with either field isolate. Root endophytic bacterial and fungal communities responded to changes in inoculation, isolate type, sampling time, and canola genotype. In contrast, fungal communities associated with the rhizosphere exhibited significant differences between sampling times, while bacterial communities associated with the rhizosphere exhibited low variability.

Levels of Empathy in Students and Professors with Patients in a Faculty of Dentistry.

BACKGROUND: Empathy is an attribute that plays an essential role in the dentist-patient therapeutic relationship, clinical care, and treatment adherence, along with providing other benefits. The main objective of this research was to establish the validity, reliability, and invariance of the Jefferson Scale of Empathy and then characterize the empathy levels of students and teachers at a dental school. MATERIALS AND METHODS: An observational and cross-sectional study analyzed a sample of undergraduate students and professors from the Universidad Andrés Bello Faculty of Dentistry (Chile) (n = 1727 and n = 267, respectively). The Empathy Scale for Health Professionals (HP) and the same scale for students (HPS) were applied. RESULTS: The Jefferson Empathy Scale presents adequate psychometric properties. The empathy measure has adequate reliability and construct validity, confirming a fit of the three-factor empathy model to the data. The measurement is invariant within the university campus, the sex of the student, and between teacher and student. Teachers present greater empathy than students except in the Perspective Adoption dimension. CONCLUSIONS: The Jefferson Empathy Scale is reliable, valid, and invariant among Chilean dental students and professors. Students do not differ from their professors in the cognitive component of empathy, but they present a lower score in the affective component and global empathy. It is inferred that students can develop the affective component of empathy in their interactions with their professors, increasing their overall empathy. Understanding and fostering empathy in dental students and professors can significantly improve patient care and treatment adherence and increase patient and dentist satisfaction.

Effects of the USA PATRIOT Act and the 2002 Bioterrorism Preparedness Act on select agent research in the United States.

A bibliometric analysis of the Bacillus anthracis and Ebola virus archival literature was conducted to determine whether negative consequences of the Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism" (USA PATRIOT) Act and the 2002 Bioterrorism Preparedness Act on US select agent research could be discerned. Indicators of the health of the field, such as number of papers published per year, number of researchers authoring papers, and influx rate of new authors, indicated an overall stimulus to the field after 2002. As measured by interorganizational coauthorships, both B. anthracis and Ebola virus research networks expanded after 2002 in terms of the number of organizations and the degree of collaboration. Coauthorship between US and non US scientists also grew for Ebola virus but contracted for the subset of B. anthracis research that did not involve possession of viable, virulent bacteria. Some non-US institutions were dropped, and collaborations with others intensified. Contrary to expectations, research did not become centralized around a few gatekeeper institutions. Two negative effects were detected. There was an increased turnover rate of authors in the select agent community that was not observed in the control organism (Klebsiella pneumoniae) research community. However, the most striking effect observed was not associated with individual authors or institutions; it was a loss of efficiency, with an approximate 2- to 5-fold increase in the cost of doing select agent research as measured by the number of research papers published per millions of US research dollars awarded.

Understanding the illicit drug distribution in England: a data-centric approach to the County Lines Model.

The County Lines Model (CLM) is a relatively new illicit drugs distribution method found in Great Britain. The CLM has brought modern slavery and public health issues, while challenging the law-enforcement capacity to act, as coordination between different local police forces is necessary. Our objective is to understand the territorial logic behind the line operators when establishing a connection between two places. We use three different spatial models (gravity, radiation and retail models), as each one of them understands flow from place i to j in a different way. Using public data from the Metropolitan Police of London, we train and cross-validate the models to understand which of the different physical and socio-demographic variables are considered when establishing a connection. We analyse hospital admissions by drugs, disposable household income, police presence and knife crime events, in addition to the population of a particular place and the distance and travel times between two different locations. Our results show that knife crime events and hospital admissions by misuse of drugs are the most important variables. We also find that London operators distribute to the territory known as the 'south' of England, as negligible presence of them is observed outside of it.

Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern.

BACKGROUND: The Amaranthus genus contains at least 20 weedy and invasive species, including Amaranthus palmeri (palmer's amaranth) and Amaranthus tuberculatus (tall waterhemp), two species of regulatory concern in North America, impacting production and yield in crops like corn, soybean and cotton. Amaranthus tuberculatus is regulated in Canada with limited establishment, while current climate models predict a range expansion of A. palmeri impacting crop growing areas in Ontario, Quebec and Manitoba. Since many Amaranthus species are similar in their morphology, especially at the seed stage, this demands the development of additional methods that can efficiently aid in the detection and identification of these species. Protein biotyping using Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) has been traditionally used to identify microorganism species, races and pathotypes. Major protein fractions extracted from an organism, ionized and run through a biotyper using mass spectrometry, result in protein spectra that represent a fingerprint at the species or lower taxonomic rank, providing an efficient molecular diagnostics method. Here we use a modified protein biotyping protocol to extract major protein fractions from seeds of the family Brassicaceae to test our protocol, and then implemented the standardized approach in seeds from Amaranthus species. We then created a database of Amaranthus protein spectra that can be used to test blind samples for a quick identification of species of concern. RESULTS: We generated a protein spectra database with 16 Amaranthus species and several accessions per species, spanning target species of regulatory concern and species which are phylogenetically related or easily confused at the seed stage due to phenotypic plasticity. Testing of two Amaranthus blind sample seed sets against this database showed accuracies of 100% and 87%, respectively. CONCLUSIONS: Our method is highly efficient in identifying Amaranthus species of regulatory concern. The mismatches between our protein biotyping approach and phenotypic identification of seeds are due to absence of the species in the database or close phylogenetic relationship between the species. While A. palmeri cannot be distinguished from A. watsonii, there is evidence these two species have the same native range and are closely related.

Quantifying the impact of COVID-19 on immigration in receiving high-income countries.

Previous studies have examined the impact of COVID-19 on mortality and fertility. However, little is known about the effect of the pandemic on constraining international migration. We use Eurostat and national statistics data on immigration and ARIMA time-series models to quantify the impact of COVID-19 on immigration flows in 15 high-income countries by forecasting their counterfactual levels in 2020, assuming no pandemic, and comparing these estimates with observed immigration counts. We then explore potential driving forces, such as stringency measures and increases in unemployment moderating the extent of immigration change. Our results show that immigration declined in all countries, except in Finland. Yet, significant cross-national variations exist. Australia (60%), Spain (45%) and Sweden (36%) display the largest declines, while immigration decreased by between 15% and 30% in seven countries, and by less than 15% in four nations where results were not statistically significant. International travel restrictions, mobility restrictions and stay-at-home requirements exhibit a relatively strong relationship with declines in immigration, although countries with similar levels of stringency witnessed varying levels of immigration decline. Work and school closings and unemployment show no relationship with changes in immigration.

AIBP regulates TRPV1 activation in chemotherapy-induced peripheral neuropathy by controlling lipid raft dynamics and proximity to TLR4 in dorsal root ganglion neurons.

ABSTRACT: Nociceptive afferent signaling evoked by inflammation and nerve injury is mediated by the opening of ligand-gated and voltage-gated receptors or channels localized to cholesterol-rich lipid raft membrane domains. Dorsal root ganglion (DRG) nociceptors express high levels of toll-like receptor 4 (TLR4), which also localize to lipid rafts. Genetic deletion or pharmacologic blocking of TLR4 diminishes pain associated with chemotherapy-induced peripheral neuropathy (CIPN). In DRGs of mice with paclitaxel-induced CIPN, we analyzed DRG neuronal lipid rafts, expression of TLR4, activation of transient receptor potential cation channel subfamily V member 1 (TRPV1), and TLR4-TRPV1 interaction. Using proximity ligation assay, flow cytometry, and whole-mount DRG microscopy, we found that CIPN increased DRG neuronal lipid rafts and TLR4 expression. These effects were reversed by intrathecal injection of apolipoprotein A-I binding protein (AIBP), a protein that binds to TLR4 and specifically targets cholesterol depletion from TLR4-expressing cells. Chemotherapy-induced peripheral neuropathy increased TRPV1 phosphorylation, localization to neuronal lipid rafts, and proximity to TLR4. These effects were also reversed by AIBP treatment. Regulation of TRPV1-TLR4 interactions and their associated lipid rafts by AIBP covaried with the enduring reversal of mechanical allodynia otherwise observed in CIPN. In addition, AIBP reduced intracellular calcium in response to the TRPV1 agonist capsaicin, which was increased in DRG neurons from paclitaxel-treated mice and in the naïve mouse DRG neurons incubated in vitro with paclitaxel. Together, these results suggest that the assembly of nociceptive and inflammatory receptors in the environment of lipid rafts regulates nociceptive signaling in DRG neurons and that AIBP can control lipid raft-associated nociceptive processing.

Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome.

BACKGROUND: Flax (Linum usitatissimum L.) is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs) are widespread in plant genomes and are a key component of their evolution. The availability of a genome assembly of flax (Linum usitatissimum) affords new opportunities to explore the diversity of TEs and their relationship to genes and gene expression. RESULTS: Four de novo repeat identification algorithms (PILER, RepeatScout, LTR_finder and LTR_STRUC) were applied to the flax genome assembly. The resulting library of flax repeats was combined with the RepBase Viridiplantae division and used with RepeatMasker to identify TEs coverage in the genome. LTR retrotransposons were the most abundant TEs (17.2% genome coverage), followed by Long Interspersed Nuclear Element (LINE) retrotransposons (2.10%) and Mutator DNA transposons (1.99%). Comparison of putative flax TEs to flax transcript databases indicated that TEs are not highly expressed in flax. However, the presence of recent insertions, defined by 100% intra-element LTR similarity, provided evidence for recent TE activity. Spatial analysis showed TE-rich regions, gene-rich regions as well as regions with similar genes and TE density. Monte Carlo simulations for the 71 largest scaffolds (≥ 1 Mb each) did not show any regional differences in the frequency of TE overlap with gene coding sequences. However, differences between TE superfamilies were found in their proximity to genes. Genes within TE-rich regions also appeared to have lower transcript expression, based on EST abundance. When LTR elements were compared, Copia showed more diversity, recent insertions and conserved domains than the Gypsy, demonstrating their importance in genome evolution. CONCLUSIONS: The calculated 23.06% TE coverage of the flax WGS assembly is at the low end of the range of TE coverages reported in other eudicots, although this estimate does not include TEs likely found in unassembled repetitive regions of the genome. Since enrichment for TEs in genomic regions was associated with reduced expression of neighbouring genes, and many members of the Copia LTR superfamily are inserted close to coding regions, we suggest Copia elements have a greater influence on recent flax genome evolution while Gypsy elements have become residual and highly mutated.

Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy.

In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca[Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree's overwintering preparations. For example, genes associated with carbon-based defences such as terpenoids were down-regulated, while many genes associated with protein-based defences and other stress mitigation mechanisms were up-regulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree's adaptive response to overwintering.