Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions.

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced small RNA (sRNA) libraries from the leaves and roots of three wheat cultivars (Kukri, RAC875 and Excalibur) under water and drought conditions. A total of 636 known miRNAs and 294 novel miRNAs were identified, of which 34 miRNAs were tissue- or cultivar-specific. Among these, 314 were significantly regulated under drought conditions. miRNAs that were drought-regulated in all cultivars displayed notably higher expression than those that responded in a cultivar-specific manner. Cultivar-specific drought response miRNAs were mainly detected in roots and showed significantly different drought regulations between cultivars. By using wheat degradome library, 6619 target genes were identified. Many target genes were strongly enriched for protein domains, such as MEKHLA, that play roles in drought response. Targeting analysis showed that drought-downregulated miRNAs targeted more genes than drought-upregulated miRNAs. Furthermore, such genes had more important functions. Additionally, the genes targeted by drought-downregulated miRNAs had multiple interactions with each other, while the genes targeted by drought-upregulated miRNAs had no interactions. Our data provide valuable information on wheat miRNA expression profiles and potential functions in different tissues, cultivars and drought conditions.

Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits.

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN ( https://pmiren.com ) does not include root tissues and root-associated miRNAs might thus be missing, we performed first the prediction of novel miRNAs using the sRNAbench tool. We found a total of 150 putatively novel miRNA genes with expression of both arms from 289 unique mature sequences and nearly 30% of all miRNA reads in roots corresponded to novel miRNAs. In contrast, this figure in leaves dropped to under 3%, confirming the undersampling of roots in the complement of known miRNAs. By using 120 publicly available wheat datasets, 598 Zea mays small RNA libraries, 64 plant species genomes, wheat degradome library, and functional enrichment analysis, a subset of novel miRNAs were confirmed as bona-fide miRNAs. Of the total 605 miRNAs identified in this study inclusive of 316 known miRNAs, 528 miRNAs were shared by both cultivars, 429 miRNAs were shared by both root tissues and 329 miRNAs were shared by both leaf tissues. In addition, 32 miRNAs were specific to Kukri while 45 miRNAs were specific to RAC875. These miRNAs had diverse functions, such as regulation of gene transcription, protein translation, energy metabolism, and cell cycle progression. Our data provide a genome-wide miRNA expression profile in these two wheat cultivars and help functional studies of wheat genomics.

Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs.

Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in I. ricinus based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick-host interaction in different tissues.

Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host.

Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host's hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for managing blood meals (storage and digestion) and protecting against host immunity and pathogen infections. Previous transcriptomic studies revealed the complexity of tick sialomes (salivary gland transcriptomes) and mialomes (midgut transcriptomes) which encode for protease inhibitors, lipocalins (histamine-binding proteins), disintegrins, enzymes, and several other tick-specific proteins. Several studies have demonstrated that mammalian hosts acquire tick resistance against repeated tick bites. Consequently, there is an urgent need to uncover how tick sialomes and mialomes respond to resistant hosts, as they may serve to develop novel tick control strategies and applications. Here, we mimicked natural repeated tick bites in a laboratory setting and analyzed gene expression dynamics in the salivary glands and midguts of adult female ticks. Rabbits were subjected to a primary (feeding on a naive host) and a secondary infestation of the same host (we re-exposed the hosts but to other ticks). We used single salivary glands and midguts dissected from individual siblings adult pathogen-free female Ixodes ricinus to reduce genetic variability between individual ticks. The comprehensive analysis of 88 obtained RNA-seq data sets allows us to provide high-quality annotated sialomes and mialomes from individual ticks. Comparisons between fed/unfed, timepoints, and exposures yielded as many as 3000 putative differentially expressed genes (DEG). Interestingly, when classifying the exposure DEGs by means of a clustering approach we observed that the majority of these genes show increased expression at early feeding time-points in the mid-gut of re-exposed ticks. The existence of clearly defined groups of genes with highly similar responses to re-exposure suggests the existence of molecular swiches. In silico functional analysis shows that these early feeding reexposure response genes form a dense interaction network at protein level being related to virtually all aspects of gene expression regulation and glycosylation. The processed data is available through an easy-to-use database-associated webpage (https://arn.ugr.es/IxoriDB/) that can serve as a valuable resource for tick research.

Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface.

Few studies have examined tick proteomes, how they adapt to their environment, and their roles in the parasite-host interactions that drive tick infestation and pathogen transmission. Here we used a proteomics approach to screen for biologically and immunologically relevant proteins acting at the tick-host interface during tick feeding and, as proof of principle, measured host antibody responses to some of the discovered candidates. We used a label-free quantitative proteomic workflow to study salivary proteomes of (i) wild Ixodes ricinus ticks fed on different hosts, (ii) wild or laboratory ticks fed on the same host, and (iii) adult ticks cofed with nymphs. Our results reveal high and stable expression of several protease inhibitors and other tick-specific proteins under different feeding conditions. Most pathways functionally enriched in sialoproteomes were related to proteolysis, endopeptidase, and amine-binding activities. The generated catalogue of tick salivary proteins enabled the selection of six candidate secreted immunogenic peptides for rabbit immunizations, three of which induced strong and durable antigen-specific antibody responses in rabbits. Furthermore, rabbits exposed to ticks mounted immune responses against the candidate peptides/proteins, confirming their expression at the tick-vertebrate interface. Our approach provides insights into tick adaptation strategies to different feeding conditions and promising candidates for developing antitick vaccines or markers of exposure of vertebrate hosts to tick bites.

sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms.

The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.

Síndrome coronario agudo y shock en el contexto de infección aguda por COVID-19 / Acute coronary syndrome and shock in the context of acute COVID-19 infection

No disponible

mirnaQC: a webserver for comparative quality control of miRNA-seq data.

Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly available miRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC.

GFET Asymmetric Transfer Response Analysis through Access Region Resistances.

Graphene-based devices are planned to augment the functionality of Si and III-V based technology in radio-frequency (RF) electronics. The expectations in designing graphene field-effect transistors (GFETs) with enhanced RF performance have attracted significant experimental efforts, mainly concentrated on achieving high mobility samples. However, little attention has been paid, so far, to the role of the access regions in these devices. Here, we analyse in detail, via numerical simulations, how the GFET transfer response is severely impacted by these regions, showing that they play a significant role in the asymmetric saturated behaviour commonly observed in GFETs. We also investigate how the modulation of the access region conductivity (i.e., by the influence of a back gate) and the presence of imperfections in the graphene layer (e.g., charge puddles) affects the transfer response. The analysis is extended to assess the application of GFETs for RF applications, by evaluating their cut-off frequency.

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.

Desarrollo perinatal del cerebro. Un paso esencial para el establecimiento de la inteligencia / Perinatal development of the brain. An essential event for the flourishing of intelligence

El desarrollo del neuroepitelio durante la etapa embrionaria es un paso obligado para el desarrollo del Sistema Nervioso Central. Sin embargo, en la especie humana el desarrollo del cerebro continúa en las cercanías del parto y, muy particularmente, durante el período postnatal inmediato. Esta última etapa del desarrollo tiene lugar de una forma destacada en la pared de los ventrículos laterales y es esencial para el refinamiento de la estructura del córtex. En este sentido, la contribución de este período del desarrollo a la complejidad del neocórtex se considera fundamental en el desarrollo de la inteligencia en la especie humana (AU)

The development of neuroepithelium during the embryonic period is a mandatory step in the CNS development. However, in the human brain development continues around birth and, particularly during the early postnatal period. During this time brain development takes place mainly in the lateral ventricle walls and results in the refining of cortex layers. Thus, the development of neocortex during postnatal period seems to be essential in the flourishing of intelligence in the human species (AU)

Treatment of diaphyseal humeral fractures with the minimally invasive percutaneous plate (MIPPO) technique: a cadaveric study and clinical results.

OBJECTIVES: To assess the clinical, functional and radiologic results of the minimally invasive percutaneous plate technique in the humerus. DESIGN: Retrospective study. SETTING: University-affiliated hospital center. PATIENTS/PARTICIPANTS: Eighty-six skeletally mature patients with humeral diaphyseal fractures requiring surgical stabilization. INTERVENTION: Treatment with locking compression plates using the minimally invasive percutaneous plate technique. MAIN OUTCOME MEASUREMENTS: Cadaveric study: distance between the plate and the neurovascular structures. Clinical outcome measurements included fracture healing, radial nerve palsy, infection, and elbow and shoulder discomfort. Radiographic measurements were time to healing, alignment, and nonunion. RESULTS: The minimum follow-up in all cases was 12 months, and all fractures except three healed. The main complications found were nonunion (three) and transitory radial nerve palsy (three). The patients recovered almost complete elbow and shoulder range of motion with 98% presenting good results; no patient had implant failure. CONCLUSIONS: The results obtained with this technique are encouraging. The technique was associated with no shoulder pain and an almost complete restitution of strength and articular range of motion. Within 6 months, 96% of the patients returned to their normal activities.

Fear avoidance beliefs influence duration of sick leave in Spanish low back pain patients.

STUDY DESIGN: Follow-up study. OBJECTIVES: To estimate the influence of fear avoidance beliefs (FAB) on 1-year low back pain (LBP)-related sick leave. SUMMARY OF BACKGROUND DATA: As opposed to Anglo-Saxon and Northern European subjects, in Spanish LBP patients the influence of FAB on disability and quality of life is virtually irrelevant. METHODS: Twelve primary care and 9 hospital services from 7 different regions of Spain recruited 165 workers who visited the National Health Service for LBP. None was excluded. On their first visit and 14 days later, patients were given 2 independent Visual Analogue Scales (VAS) for LBP and leg pain, as well as the validated Spanish versions of the Fear Avoidance Beliefs (FABQ), Roland-Morris (RMQ), and SF-12 questionnaires. During the following 12-month period, the number of days on sick leave because of LBP was registered. RESULTS: Differences in sick leave throughout the study period were associated with baseline differences in chronicity, severity of low back (not referred) pain, disability, FAB, physical and mental quality of life, being on sick leave when entering the study, and duration of previous sick leave. Ordinal logistic regression models showed that each additional point in the total FAB baseline score increases by 2.4% the odds of being on sick leave for up to 60 days during the following year and by 7.7% the odds of being sick listed for 61 days or more. Corresponding figures for FAB-Work scores are 4.2% and 11%. No variable modifies the effect of FAB on sick leave. CONCLUSION: Although in Spanish patients the influence of FAB on disability and quality of life is irrelevant, baseline FABQ score does influence LBP-related sick leave during the following year. This seems to be a direct effect of FAB, since there is no confounding by any other variable.

Psychometric characteristics of the Spanish version of the FAB questionnaire.

STUDY DESIGN: Validation of a translated, culturally adapted questionnaire. OBJECTIVES: To translate and culturally adapt the Spanish version of the Fear Avoidance Beliefs Questionnaire (FABQ), and to validate its use in Spanish-speaking patients with low back pain (LBP). SUMMARY OF BACKGROUND DATA: The FABQ is a reliable evaluation instrument for fear avoidance beliefs, which includes two subscales (FAB-Work and FAB-Phys). No validated Spanish version was available. METHODS: Translation/retranslation of the English version of the FABQ was done blindly and independently by a multidisciplinary team. The study was done in 12 primary care centers and 9 hospital outpatient clinics from seven regions in Spain, with 209 acute, subacute, and chronic patients who visited their physician for LBP: 53 in the pilot phase and 156 in the validation phase. Subjects were given the FABQ, two VAS for LBP and referred pain, and the Roland-Morris and SF-12 Questionnaires on their first visit and 14 days later. In the pilot phase, on day 1 test-retest reliability was estimated by giving a second FABQ in which the name and order of the items had been changed. RESULTS: Time necessary to complete the FABQ was [median, P25, P75] 10 minutes (5,15). FABQ values were not normally distributed. Comprehensibility: No request for aid in interpretation was made during the validation phase and no item was left unanswered by >or= 10% of patients. Reliability: Scores [median, P25, P75] of the two FABQ were: 72.00 (47.25, 82.00) and 72.00 (49.50, 83.75), with an intraclass correlation coefficient of 0.9668 (95% confidence interval, 0.9421,0.9823). Mean of kappa values for all items was 0.743. Internal Consistency: Cronbach's alpha was 0.9337. VALIDITY: Values of FAB and FAB-Work were >37% higher for patients on sick leave. For FAB-Phys differences were below 8%. FABQ, FAB-Work and FAB-Phys strongly correlated with disability on days 1 and 15. CONCLUSIONS: The Spanish version of the FABQ has good comprehensibility, internal consistency, and reliability. It cannot be analyzed parametrically, but only nonparametrically. The total FABQ is at least as valid as its subscales and simpler to score, making it more suitable for routine clinical use.

The influence of fear avoidance beliefs on disability and quality of life is sparse in Spanish low back pain patients.

STUDY DESIGN: Correlation between previously validated questionnaires. OBJECTIVES: To assess the influence of fear avoidance beliefs (FAB) on disability and quality of life in Spanish low back pain (LBP) patients. SUMMARY OF BACKGROUND DATA: FAB has shown to be a major determinant of disability in LBP patients in Northern European and Anglo-Saxon cultural environments. There are no data on its influence on Latin-Mediterranean patients. METHODS: The study was done in 12 primary care and 9 hospital services from seven different regions of Spain, with 209 patients who were in a potentially active working situation and visited the National Health Service for LBP. None was excluded and the sample was balanced for acute, subacute, and chronic patients. On their first visit and 14 days later, patients were given two independent Visual Analogue Scales (VAS) for LBP and leg pain, as well as the validated Spanish versions of the Fear Avoidance Beliefs (FABQ), Roland-Morris (RMQ), and SF-12 questionnaires. RESULTS: Correlations between LBP, leg pain, FABQ, disability, and quality of life were moderate on day 1 (r = 0.320-0.564) and stronger on day 15 (r = 0.457-0.637). All of them were statistically highly significant (P = 0.000). Regression models showed that LBP severity explains 33% of disability on day 1 and 20% on day 15, while FAB only explains 6% on day 1 and 2% on day 15. FAB does not explain mental quality of life. It explains only 5% of physical quality of life on day 1 and 4% on day 15. There was no interaction between FAB and chronicity, and FABQ values on day 1 did not predict disability or quality of life at day 15. CONCLUSIONS: As opposed to what has been shown in other cultural settings, FAB have virtually no clinical relevance in Spanish LBP patients who are treated in the National Health Service and who are in a potentially active working situation. The influence of FAB on disability is minimal and much less than that of pain severity, and their contribution to the patient's quality of life is irrelevant. Further studies should explore the potential value of FAB in other Latin-Mediterranean countries.

Resultados del tratamiento en pacientes con diagnóstico de Mal de Pott. Hospital Escuela Lenín Fonseca, servicio de ortopedia y traumatología. 1997-2002 / Results of the treatment in patient with diagnostic of Evil of Pott. School Hospital Lenín Fonseca, orthopedics service and traumatología. 1997-2002

Se evaluaron 25 pacientes con impresión diagnóstica de Mal de Pott ingresados al servicio de Ortopedia y Traumatología del Hospital Escuela Lenín Fonseca, entre Enero 1997 a Diciembre 2002. Encontramos que la mayoria de pacientes afectados se encuentran entre los 35 ños, y que la mayor parte proviene de las zonas rurales de nuestro país. El espinal más afectado fue el raquis toraco lumbar (TI 1 - L2), y la mayor ie los casos estaban en estadio de Surrel I; los pacientes del estudio recibieron tratamiento antifímico según edad y mas establecidos. El 88 porciento de pacientes fue sometido a procedimiento quirúrgico mediante abordaje anterior tipo Hodgson-Stock mas injerto en tirante. En la mayor parte de los casos la cirugía duró tiempo promedio más de dos horas. La mayoria de los casos presentó una deformidad en cifosis moderada (11 a 29 os) con un estado neurológico Frankel 01 ó 02. Después del procedimiento quirúrgico la deformidad pasó a ser cifosis leve (O a 10 grados). Serealizó un seguimiento de los casos al año de la cirugía. Se encontró que la mayor parte de los casos tenía una deformidad en cifosis moderada pero con estado neurológico Franket E. Los pacientes que no fueron sometidos a cirugía se les realizó seguimiento al año deldiagnóstico. Se encontró que tenían una mayor deformidad en cifosis comparación a la del ingreso y una regresión del estado neurológico...