A circular RNA vector for targeted plant gene silencing based on an asymptomatic viroid.

Gene silencing for functional studies in plants has been largely facilitated by manipulating viral genomes with inserts from host genes to trigger virus-induced gene silencing (VIGS) against the corresponding mRNAs. However, viral genomes encode multiple proteins and can disrupt plant homeostasis by interfering with endogenous cell mechanisms. To try to circumvent this functional limitation, we have developed a silencing method based on the minimal autonomously-infectious nucleic acids currently known: viroids, which lack proven coding capability. The genome of Eggplant latent viroid, an asymptomatic viroid, was manipulated with insertions ranging between 21 and 42 nucleotides. Our results show that, although larger insertions might be tolerated, the maintenance of the secondary structure appears to be critical for viroid genome stability. Remarkably, these modified ELVd molecules are able to induce systemic infection promoting the silencing of target genes in eggplant. Inspired by the design of artificial microRNAs, we have developed a simple and standardized procedure to generate stable insertions into the ELVd genome capable of silencing a specific target gene. Analogously to VIGS, we have termed our approach viroid-induced gene silencing, and demonstrate that it is a promising tool for dissecting gene functions in eggplant.

Integrative time-scale and multi-omics analysis of host responses to viroid infection.

Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.

Identification and management of tomato brown rugose fruit virus in greenhouses in Mexico.

Tomato brown rugose fruit virus (ToBRFV) has become a cause of great concern in the global tomato agro-industry since its first report in Israel in 2014. Global tomato production is affected by ToBRFV, and management practices are being evaluated. We tested seed lots from international producers as well as greenhouse substrates and water wells as possible sources of virus contamination. We identified a second introduction of ToBRFV in Mexico by a strain closely resembling isolates from the Netherlands and the Middle East. ToBRFV was detected by RT-PCR in seed coats and epicotyls (from commercial seeds and seedlings obtained from infected tomato plants), indicating a transmission rate of 9%. Virus-like particles (VLPs) were found in wells used for irrigation in greenhouses, but these exhibited low infectivity. These findings suggest that water sources could serve as ToBRFV reservoirs. We evaluated four chemical and six thermal methods for sanitizing substrates, plasticware, and other greenhouse utensils, using detached leaf bioassays in Nicotiana rugosa. The most effective chemical sanitization method was treatment with glutaraldehyde plus quaternary ammonium salts and pentapotassium salts. The most effective heat treatment was at 92°C for 30 minutes, which inactivated the virus. Tomato producers could implement these sanitization methods to control ToBRFV.

Fuzzy Synchronization of Chaotic Systems with Hidden Attractors.

Chaotic systems are hard to synchronize, and no general solution exists. The presence of hidden attractors makes finding a solution particularly elusive. Successful synchronization critically depends on the control strategy, which must be carefully chosen considering system features such as the presence of hidden attractors. We studied the feasibility of fuzzy control for synchronizing chaotic systems with hidden attractors and employed a special numerical integration method that takes advantage of the oscillatory characteristic of chaotic systems. We hypothesized that fuzzy synchronization and the chosen numerical integration method can successfully deal with this case of synchronization. We tested two synchronization schemes: complete synchronization, which leverages linearization, and projective synchronization, capitalizing on parallel distributed compensation (PDC). We applied the proposal to a set of known chaotic systems of integer order with hidden attractors. Our results indicated that fuzzy control strategies combined with the special numerical integration method are effective tools to synchronize chaotic systems with hidden attractors. In addition, for projective synchronization, we propose a new strategy to optimize error convergence. Furthermore, we tested and compared different Takagi-Sugeno (T-S) fuzzy models obtained by tensor product (TP) model transformation. We found an effect of the fuzzy model of the chaotic system on the synchronization performance.

WNT/ß-catenin modulates the axial identity of embryonic stem cell-derived human neural crest.

WNT/ß-catenin signaling is crucial for neural crest (NC) formation, yet the effects of the magnitude of the WNT signal remain ill-defined. Using a robust model of human NC formation based on human pluripotent stem cells (hPSCs), we expose that the WNT signal modulates the axial identity of NCs in a dose-dependent manner, with low WNT leading to anterior OTX+ HOX- NC and high WNT leading to posterior OTX- HOX+ NC. Differentiation tests of posterior NC confirm expected derivatives, including posterior-specific adrenal derivatives, and display partial capacity to generate anterior ectomesenchymal derivatives. Furthermore, unlike anterior NC, posterior NC exhibits a transient TBXT+/SOX2+ neuromesodermal precursor-like intermediate. Finally, we analyze the contributions of other signaling pathways in posterior NC formation, which suggest a crucial role for FGF in survival/proliferation, and a requirement of BMP for NC maturation. As expected retinoic acid (RA) and FGF are able to modulate HOX expression in the posterior NC. Surprisingly, early RA supplementation prohibits NC formation. This work reveals for the first time that the amplitude of WNT signaling can modulate the axial identity of NC cells in humans.

Timed up and go test predicts mortality in older adults in Peru: a population-based cohort study.

BACKGROUND: While there is evidence about stablished risk factors (e.g., raised blood pressure) and higher mortality risk in older population, less has been explored about other functional parameters like the Timed Up and Go test and the Gait Speed in older people at low- and middle-income countries. We aimed to study these mobility tests as predictors of mortality in a population of older people in Peru. METHODS: Population-based prospective cohort study (2013-2020). Random sampling of people aged 60+ years in a community of Lima, Peru. Geriatricians conducted all clinical evaluations and laboratory tests were conducted in the local hospital. Participants were sought in the national vital registration system, and we collated cause (ICD-10) and date of death. We conducted a nested forward multivariate Cox proportional hazard model to identify all potential predictors of all-cause, communicable and non-communicable diseases mortality. RESULTS: At baseline, there were 501 older people (mean age 70.6 and 62.8% were women), complete follow-up information was available from 427 people. Mean follow-up time was 46.5 months (SD = 25.3). In multivariate models, the Timed Up and Go test was associated with higher risk of all-cause mortality (HR = 1.05; 95% CI: 1.02-1.09). For cause-specific mortality, history of heart disease (HR = 2.25; 95% CI: 1.07-4.76) and age in years (HR = 1.05; 95% CI: 1.01-1.09) were predictors of non-communicable diseases mortality. CONCLUSIONS: In addition to established risk factors for mortality in older population, the Timed Up and Go test, a functional parameter, raised as a relevant predictor of all-cause mortality.

Measurement of the Spectral Efficiency of a Heterogeneous Network Architecture of the NG-PON Type for a Quasilinear Propagation Regime.

The objective of future optical fiber networks is to provide an efficient infrastructure capable of supporting an increasing and variable number of data traffic generated by the diversification of applications with different speed requirements that the current legacy Line Speed networks Single Line Rate (SLR), with predefined modulation formats, cannot supply, because they do not offer enough flexibility to meet the requirements of the demands with such a wide range of granularities. Therefore, next-generation optical networks will be highly heterogeneous in nature, incorporating mixed modulation formats and Mixed Line Rates (MLR). In this work, an analysis of the measurement of the spectral efficiency of a heterogeneous network architecture of the next-generation passive optical network (NG-PON) type is reported for a quasilinear propagation regime through the use of the equation adapted from Shannon's information theory and developed by the group from the GNTT Research of the University of Cauca, where it was found that it is better to transmit channels of 10 Gbps and 40 Gbps with robust modulations in MLR networks to make an improvement in the spectral efficiency of the network, achieving the same amount of information in a smaller bandwidth or more information in the same bandwidth.

Localization accuracy of a common beamformer for the comparison of two conditions.

The linearly constrained minimum variance beamformer is frequently used to reconstruct sources underpinning neuromagnetic recordings. When reconstructions must be compared across conditions, it is considered good practice to use a single, "common" beamformer estimated from all the data at once. This is to ensure that differences between conditions are not ascribable to differences in beamformer weights. Here, we investigate the localization accuracy of such a common beamformer. Based on theoretical derivations, we first show that the common beamformer leads to localization errors in source reconstruction. We then turn to simulations in which we attempt to reconstruct a (genuine) source in a first condition, while considering a second condition in which there is an (interfering) source elsewhere in the brain. We estimate maps of mislocalization and assess statistically the difference between "standard" and "common" beamformers. We complement our findings with an application to experimental MEG data. The results show that the common beamformer may yield significant mislocalization. Specifically, the common beamformer may force the genuine source to be reconstructed closer to the interfering source than it really is. As the same applies to the reconstruction of the interfering source, both sources are pulled closer together than they are. This observation was further illustrated in experimental data. Thus, although the common beamformer allows for the comparison of conditions, in some circumstances it introduces localization inaccuracies. We recommend alternative approaches to the general problem of comparing conditions.

Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants.

Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to turnip mosaic potyvirus, with a more efficient response against the ancestral isolate. In wild-type plants, both isolates induced similar levels of cytosine methylation changes, including in and around transposable elements and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.

Might exogenous circular RNAs act as protein-coding transcripts in plants?

Circular RNAs (circRNAs) are regulatory molecules involved in the modulation of gene expression. Although originally assumed as non-coding RNAs, recent studies have evidenced that animal circRNAs can act as translatable transcripts. The study of plant-circRNAs is incipient, and no autonomous coding plant-circRNA has been described yet. Viroids are the smallest plant-pathogenic circRNAs known to date. Since their discovery 50 years ago, viroids have been considered valuable systems for the study of the structure-function relationships in RNA, essentially because they have not been shown to have coding capacity. We used two pathogenic circRNAs (Hop stunt viroid and Eggplant latent viroid) as experimental tools to explore the coding potential of plant-circRNAs. Our work supports that the analysed viroids contain putative ORFs able to encode peptides carrying subcellular localization signals coincident with the corresponding replication-specific organelle. Bioassays in well-established hosts revealed that mutations in these ORFs diminish their biological efficiency. Interestingly, circular forms of HSVd and ELVd were found to co-sediment with polysomes, revealing their physical interaction with the translational machinery of the plant cell. Based on this evidence we hypothesize about the possibility that plant circRNAs in general, and viroids in particular, can act, under certain cellular conditions, as non-canonical translatable transcripts.

A Practical Approach to Diagnosis of Spinal Dysraphism.

Spinal dysraphisms (SDs) are congenital malformations of the spinal cord, determined by derangement in the complex cascade of embryologic events involved in spinal development. They represent a heterogeneous group ranging from mild clinical manifestations-going unnoticed or being discovered at clinical examination-to a causal factor of life quality impairment, especially when associated with musculoskeletal, gastrointestinal, genitourinary, or respiratory system malformations. Knowledge of the normal embryologic development of the spinal cord-which encompasses three main steps (gastrulation, primary neurulation, and secondary neurulation)-is crucial for understanding the pathogenesis, neuroradiologic scenarios, and clinical-radiologic classification of congenital malformations of the spinal cord. SDs can be divided with clinical examination or neuroradiologic study into two major groups: open SDs and closed SDs. Congenital malformations of the spinal cord include a wide range of abnormalities that vary considerably in imaging and clinical characteristics and complexity and therefore may represent a diagnostic challenge, even for the experienced radiologist. Online supplemental material is available for this article. ©RSNA, 2021.

Symptom Severity, Infection Progression and Plant Responses in Solanum Plants Caused by Three Pospiviroids Vary with the Inoculation Procedure.

Infectious viroid clones consist of dimeric cDNAs used to generate transcripts which mimic the longer-than-unit replication intermediates. These transcripts can be either generated in vitro or produced in vivo by agro-inoculation. We have designed a new plasmid, which allows both inoculation methods, and we have compared them by infecting Solanum lycopersicum and Solanum melongena with clones of Citrus exocortis virod (CEVd), Tomato chlorotic dwarf viroid (TCDVd), and Potato spindle tuber viroid (PSTVd). Our results showed more uniform and severe symptoms in agro-inoculated plants. Viroid accumulation and the proportion of circular and linear forms were different depending on the host and the inoculation method and did not correlate with the symptoms, which correlated with an increase in PR1 induction, accumulation of the defensive signal molecules salicylic (SA) and gentisic (GA) acids, and ribosomal stress in tomato plants. The alteration in ribosome biogenesis was evidenced by both the upregulation of the tomato ribosomal stress marker SlNAC082 and the impairment in 18S rRNA processing, pointing out ribosomal stress as a novel signature of the pathogenesis of nuclear-replicating viroids. In conclusion, this updated binary vector has turned out to be an efficient and reproducible method that will facilitate the studies of viroid-host interactions.

Human neural crest induction by temporal modulation of WNT activation.

The developmental biology of neural crest cells in humans remains unexplored due to technical and ethical challenges. The use of pluripotent stem cells to model human neural crest development has gained momentum. We recently introduced a rapid chemically defined approach to induce robust neural crest by WNT/ß-CATENIN activation. Here we investigate the temporal requirements of ectopic WNT activation needed to induce neural crest cells. By altering the temporal activation of canonical WNT/ß-CATENIN with a GSK3 inhibitor we find that a 2 Day pulse of WNT/ß-CATENIN activation via GSK3 inhibition is optimal to generate bona fide neural crest cells, as shown by their capacity to differentiate to neural crest specific fates including peripheral neurons, glia, melanoblasts and ectomesenchymal osteocytes, chondrocytes and adipocytes. Although a 2 Day pulse can impart neural crest character when GSK3 is inhibited days after seeding, optimal results are obtained when WNT is activated from the beginning, and we find that the window of competence to induce NCs from non-neural ectodermal/placodal precursors closes by day 3 of culture. The reduced requirement for exogenous WNT activation offers an approach that is cost-effective, and we show that this adherent 2-dimensional approach is efficient in a broad range of culture platforms ranging from 96-well vessels to 10 cm dishes.

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon.

miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.

Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon.

Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of nonidentical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse environmental conditions is limited. Here, we provide the first comprehensive analysis of computationally inferred melon-tasiRNAs responsive to two biotic (viroid-infection) and abiotic (cold treatment) stress conditions. We identify two TAS3-loci encoding to length (TAS3-L) and short (TAS3-S) transcripts. The TAS candidates predicted from small RNA-sequencing data were characterized according to their chromosome localization and expression pattern in response to stress. The functional activity of cmTAS genes was validated by transcript quantification and degradome assays of the tasiRNA precursors and their predicted targets. Finally, the functionality of a representative cmTAS3-derived tasiRNA (TAS3-S) was confirmed by transient assays showing the cleavage of ARF target transcripts.

WNT/ß-catenin signaling mediates human neural crest induction via a pre-neural border intermediate.

Neural crest (NC) cells arise early in vertebrate development, migrate extensively and contribute to a diverse array of ectodermal and mesenchymal derivatives. Previous models of NC formation suggested derivation from neuralized ectoderm, via meso-ectodermal, or neural-non-neural ectoderm interactions. Recent studies using bird and amphibian embryos suggest an earlier origin of NC, independent of neural and mesodermal tissues. Here, we set out to generate a model in which to decipher signaling and tissue interactions involved in human NC induction. Our novel human embryonic stem cell (ESC)-based model yields high proportions of multipotent NC cells (expressing SOX10, PAX7 and TFAP2A) in 5 days. We demonstrate a crucial role for WNT/ß-catenin signaling in launching NC development, while blocking placodal and surface ectoderm fates. We provide evidence of the delicate temporal effects of BMP and FGF signaling, and find that NC development is separable from neural and/or mesodermal contributions. We further substantiate the notion of a neural-independent origin of NC through PAX6 expression and knockdown studies. Finally, we identify a novel pre-neural border state characterized by early WNT/ß-catenin signaling targets that displays distinct responses to BMP and FGF signaling from the traditional neural border genes. In summary, our work provides a fast and efficient protocol for human NC differentiation under signaling constraints similar to those identified in vivo in model organisms, and strengthens a framework for neural crest ontogeny that is separable from neural and mesodermal fates.

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon.

BACKGROUND: MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited. RESULTS: Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development. CONCLUSION: Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon.

Vitamin D Level and Supplementation in Pediatric Atopic Dermatitis: A Randomized Controlled Trial.

BACKGROUND:: Atopic dermatitis (AD) is a chronic inflammatory skin condition characterized by a pruritic eczematous rash. Evidence surrounding the role of serum vitamin D (VD) in modifying disease severity is inconsistent. OBJECTIVES:: To determine whether VD levels are correlated with AD severity and the effects of VD supplementation on disease modification. METHODS:: This was a 2-phase study, using a cross-sectional design to evaluate the relationship between VD level and severity, as well as a double-blinded, randomized control trial to elucidate the effects of VD supplementation. Patients aged 0 to 18 years with AD were included in phase 1, and disease severity and serum VD levels were determined. Those with renal, liver, or other dermatologic conditions were excluded. Patients with abnormal (<72.7 nmol/L) VD levels were eligible for phase 2 and to be randomized to either VD supplementation of 2000 IU/d or placebo. VD level and severity were assessed at baseline and 3 months. RESULTS:: The 77 patients included in phase 1 had a mean (SD) age of 7.4 (4.5) years, and 45.5% (33/77) were female. Increased severity was significantly correlated with lower VD levels ( P = .015). Of the 45 patients included in phase 2, 21 and 24 were assigned to the supplementation and placebo arm, respectively. The mean (SD) change in severity did not differ significantly between the supplementation (15.35 [9.71]) and placebo (15.13 [8.97]) groups after 3 months of intervention ( P = .7). CONCLUSION:: Although VD levels correlated with AD severity, VD supplementation did not significantly improve disease severity.

A Monocular SLAM-based Controller for Multirotors with Sensor Faults under Ground Effect.

Multirotor micro air vehicles can operate in complex and confined environments that are otherwise inaccessible to larger drones. Operation in such environments results in airflow interactions between the propellers and proximate surfaces. The most common of these interactions is the ground effect. In addition to the increment in thrust efficiency, this effect disturbs the onboard sensors of the drone. In this paper, we present a fault-tolerant scheme for a multirotor with altitude sensor faults caused by the ground effect. We assume a hierarchical control structure for trajectory tracking. The structure consists of an external Proportional-Derivative controller and an internal Proportional-Integral controller. We consider that the sensor faults occur on the inner loop and counteract them in the outer loop. In a novel approach, we use a metric monocular Simultaneous Localization and Mapping algorithm for detecting internal faults. We design the fault diagnosis scheme as a logical process which depends on the weighted residual. Furthermore, we propose two control strategies for fault mitigation. The first combines the external PD controller and a function of the residual. The second treats the sensor fault as an actuator fault and compensates with a sliding mode action. In either case, we utilize onboard sensors only. Finally, we evaluate the effectiveness of the strategies in simulations and experiments.