Estimating Transcriptome Diversity and Specialization in Capsicum annuum L

Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.

A non-invasive method to predict drought survival in Arabidopsis using quantum yield under light conditions

BACKGROUND

Survival rate (SR) is frequently used to compare drought tolerance among plant genotypes. While a variety of techniques for evaluating the stress status of plants under drought stress conditions have been developed, determining the critical point for the recovery irrigation to evaluate plant SR often relies directly on a qualitative inspection by the researcher or on the employment of complex and invasive techniques that invalidate the subsequent use of the tested individuals.

RESULTS

Here, we present a simple, instantaneous, and non-invasive method to estimate the survival probability of Arabidopsis thaliana plants after severe drought treatments. The quantum yield (QY), or efficiency of photosystem II, was monitored in darkness (Fv/Fm) and light (Fv'/Fm') conditions in the last phase of the drought treatment before recovery irrigation. We found a high correlation between a plant's Fv'/Fm' value before recovery irrigation and its survival phenotype seven days after, allowing us to establish a threshold between alive and dead plants in a calibration stage. This correlation was maintained in the Arabidopsis accessions Col-0, Ler-0, C24, and Kondara under the same conditions. Fv'/Fm' was then applied as a survival predictor to compare the drought tolerance of transgenic lines overexpressing the transcription factors ATAF1 and PLATZ1 with the Col-0 control.

CONCLUSIONS

The results obtained in this work demonstrate that the chlorophyll a fluorescence parameter Fv'/Fm' can be used as a survival predictor that gives a numerical estimate of the Arabidopsis drought SR before recovery irrigation. The procedure employed to get the Fv'/Fm' measurements is fast, non-destructive, and requires inexpensive and easy-to-handle equipment. Fv'/Fm' as a survival predictor can be used to offer an overview of the photosynthetic state of the tested plants and determine more accurately the best timing for rewatering to assess the SR, especially when the symptoms of severe dehydration between genotypes are not contrasting enough to identify a difference visually.

Large scale sampling of Mexican maize landraces for the presence of transgenes

The presence and levels of transgenic maize in Mexico and the effect this could have on local landraces or closely related species such as teosinte has been the subject of several previous reports, some showing contrasting results. Cultural, social and political factors all affect maize cultivation in Mexico and although since 1998 there has been a moratorium on the commercial cultivation of transgenic maize, Mexico imports maize, mainly from the USA where transgenic cultivars are widely grown. Additionally extensive migration between rural areas in Mexico and the USA and customs of seed exchange between farmers may also play an unintentional role in the establishment of transgenic seed. A comprehensive study of all Mexican maize landraces throughout the country is not feasible, however this report presents data based on analysis of 3204 maize accessions obtained from the central region of Mexico (where permits have never been authorized for cultivation of transgenic maize) and the northern region (where for a short period authorization for experimental plots was granted). The results of the study confirm that transgenes are present in all the geographical areas sampled and were more common in germplasm obtained in the northern region. However, there was no evidence that regions where field trials had been authorized showed higher levels of transgene presence or that the morphology of seed lots harboring transgenic material was significantly modified in favor of expected transgenic phenotypes.

Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.)

Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).

Non-convulsive status epilepticus as the initial manifestation in a family with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an autosomal dominant small-vessel disease caused by mutations of the NOTCH3 gene. It typically presents with migraine, recurrent brain ischaemia, and cognitive disorders. Seizures rarely present as the initial manifestation, with non-convulsive status epilepticus being even less frequent. We present a series of 3 related patients with this arteriopathy, 2 of whom presented status epilepticus as a manifestation of the disease.

Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis

During the ripening process, the pericarp of chili pepper (Capsicum spp.) fruits accumulates large amounts of carotenoids. Although the carotenoid biosynthesis pathway in the Capsicum genus has been widely studied from different perspectives, the transcriptional regulation of genes encoding carotenoid biosynthetic enzymes has not been elucidated in this fruit. We analyzed RNA-Seq transcriptomic data from the fruits of 12 accessions of Capsicum annuum during the growth, development, and ripening processes using the R package named Salsa. We performed coexpression analyses between the standardized expression of genes encoding carotenoid biosynthetic enzymes (target genes (TGs)) and the genes of all expressed transcription factors (TFs). Additionally, we analyzed the promoter region of each biosynthetic gene to identify putative binding sequences for each selected TF candidate. We selected 83 TFs as putative regulators of the carotenogenic structural genes. From them, putative binding sites in the promoters of the carotenoid-biosynthesis-related structural genes were found for only 54 TFs. These results could guide the search for transcription factors involved in the regulation of the carotenogenic pathway in chili pepper fruits and might facilitate the collection of corresponding experimental evidence to corroborate their participation in the regulation of this biosynthetic pathway in Capsicum spp.

Metabolomic Analysis Identifies Differences Between Wild and Domesticated Chili Pepper Fruits During Development (Capsicum annuum L.)

Capsicum spp. members are a rich source of specialized compounds due to their secondary metabolism. Some metabolic pathways have suffered modifications during the domestication process and improvement of agricultural traits. Here, we compared non-targeted LC-MS profiles from several areas: wild accessions (C. annuum L. var. glabriusculum), domesticated cultivars (C. annuum L.), and the F1 progeny of a domesticated, and a wild accession cross (in both directions) throughout seven stages of fruit development of chili pepper fruits. The main detected differences were in glycerophospholipid metabolism, flavone and flavonol biosynthesis, sphingolipid metabolism, and cutin biosynthesis. The domesticated group exhibited a higher abundance in 12'-apo-β-carotenal, among others capsorubin, and β-tocopherol. Palmitic acid and derivates, terpenoids, and quercitrin were prevalent in the wild accessions. F1 progeny showed a higher abundance of capsaicin, glycol stearate, and soyacerebroside I. This work supports evidence of the side-affectation of trait selection over the metabolism of chili pepper fruit development. Furthermore, it was also observed that there was a possible heterosis effect over the secondary metabolism in the F1 progeny.

Impact of an enhanced screening program on the detection of non-AIDS neoplasias in patients with human immunodeficiency virus infection

BACKGROUND

The incidence of non-AIDS defining cancer (NADC) is higher in people living with HIV (PLWH) than in the general population, and it is already one of the leading causes of death in the HIV-infected population. It is estimated that the situation will be aggravated by the progressive aging of PLWH. Early diagnosis through intensive cancer screening may improve the ability for therapeutic interventions and could be critical in reducing mortality, but it might also increase expenditure and harms associated with adverse events. The aim of this study is to evaluate an enhanced screening program for early diagnosis of cancer in PLWH compared to standard practice. The specific objectives are (1) to compare the frequency of cancer diagnosed at an early stage, (2) to analyze safety of the enhanced program: adverse events and unnecessary interventions, (3) to analyze the cost-utility of the program, and (4) to estimate the overall and site-specific incidence of NADC in PLWH.

METHODS

We will conduct a multicenter, non-blinded, randomized, controlled trial, comparing two parallel arms: conventional vs enhanced screening. Data will be recorded in an electronic data collection notebook. Conventional intervention group will follow the standard of care screening in the participating centers, according to the European AIDS Clinical Society recommendations, and the enhanced intervention group will follow an expanded screening aimed to early detection of lung, liver, anal, cervical, breast, prostate, colorectal, and skin cancer. The trial will be conducted within the framework of the Spanish AIDS Research Network Cohort (CoRIS).

DISCUSSION

The trial will evaluate the efficacy, safety, and efficiency of an enhanced screening program for the early diagnosis of cancer in HIV patients compared to standard of care practice. The information provided will be relevant since there are currently no studies on expanded cancer screening strategies in patients with HIV, and available data estimating cost effectiveness or cost-utility of such as programs are scarce. An enhanced program for NADC screening in patients with HIV could lead to early diagnosis and improve the prognosis of these patients, with an acceptable rate of unnecessary interventions, but it is critical to demonstrate that the benefits clearly outweigh the harms, before the strategy could be implemented.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04735445. Registered on 25 June 2019.

Inheritance of gene expression throughout fruit development in chili pepper

Gene expression is the primary molecular phenotype and can be estimated in specific organs or tissues at particular times. Here we analyzed genome-wide inheritance of gene expression in fruits of chili pepper (Capsicum annuum L.) in reciprocal crosses between a domesticated and a wild accession, estimating this parameter during fruit development. We defined a general hierarchical schema to classify gene expression inheritance which can be employed for any quantitative trait. We found that inheritance of gene expression is affected by both, the time of fruit development as well as the direction of the cross, and propose that such variations could be common in many developmental processes. We conclude that classification of inheritance patterns is important to have a better understanding of the mechanisms underlying gene expression regulation, and demonstrate that sets of genes with specific inheritance pattern at particular times of fruit development are enriched in different biological processes, molecular functions and cell components. All curated data and functions for analysis and visualization are publicly available as an R package.

Music therapy and Sanfilippo syndrome: an analysis of psychological and physiological variables of three case studies

Introduction

Mucopolysaccharidosis type III (MPS III) or Sanfilippo syndrome is a neurodegenerative disease caused by the accumulation of mucopolysaccharides in the body. As the symptoms are wide ranging, it is a challenge to provide a diagnosis and psychological treatment for affected children.

Method

The main objective of this study was to describe a form of music therapy treatment applied to three children diagnosed with MPS III. The psychological variables were evaluated by an ad hoc observation recording template, and the physiological variables were measured with a digital meter before and after each session. The perception of the parents was also considered through a semi-structured interview.

Results

An improvement in the psychological variables was shown in all cases. Changes in the physiological variables were also noted, although they varied according to each child. The parents report some benefit of music therapy and they share difficulty in assessing the extent of benefits of the music therapy.

Discussion

Findings indicate that music therapy can be a useful form of treatment with multiple benefits for children with conditions such as MPS III or similar conditions. However, further research is needed in this area and in the development of specific ways of evaluating music therapy.

Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.

A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

Ketogenic diet and cognition in neurological diseases: a systematic review

CONTEXT

In recent years, the ketogenic diet has gained special relevance as a possible therapeutic alternative to some neurological and chronic diseases.

OBJECTIVE

The aim of this systematic review was to answer the following question: Does a ketogenic diet improve cognitive skills in patients with Alzheimer's disease, Parkinson's disease, refractory epilepsy, and type 1 glucose deficiency syndrome? To define the research question, the PICOS criteria were used, following the guidelines of the PRISMA method.

DATA SOURCES

Medline/PubMed, Elsevier Science Direct, Dialnet, EBSCOhost, Mediagraphic, Sage Journals, ProQuest, and Wiley Online Library databases were used.

DATA EXTRACTION

After applying inclusion and exclusion criteria in accordance with the PRISMA method, a total of 63 entries published between 2004 and 2019 were used.

DATA ANALYSIS

The records extracted were analyzed from a qualitative approach, so no statistical analysis was carried out.

CONCLUSION

Although scientific literature on the subject is scarce and there has tended to be a lack of scientific rigor, the studies reviewed confirmed the effectiveness of this diet in improving the cognitive symptomatology of the aforementioned diseases.

Non-convulsive status epilepticus as the initial manifestation in a family with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an autosomal dominant small-vessel disease caused by mutations of the NOTCH3 gene. It typically presents with migraine, recurrent brain ischaemia, and cognitive disorders. Seizures rarely present as the initial manifestation, with non-convulsive status epilepticus being even less frequent. We present a series of 3 related patients with this arteriopathy, 2 of whom presented status epilepticus as a manifestation of the disease.

Compacta: a fast contig clustering tool for de novo assembled transcriptomes

Background

RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these transcripts. However, for unknown genomes, de novo assembly of RNA-Seq reads must be performed to generate a set of contigs that represents the transcriptome. These contig sets contain multiple transcripts, including immature mRNAs, spliced transcripts and allele variants, as well as products of close paralogs or gene families that can be difficult to distinguish. Thus, tools are needed to select a set of less redundant contigs to represent the transcriptome for downstream analyses. Here we describe the development of Compacta to produce contig sets from de novo assemblies.

Results

Compacta is a fast and flexible computational tool that allows selection of a representative set of contigs from de novo assemblies. Using a graph-based algorithm, Compacta groups contigs into clusters based on the proportion of shared reads. The user can determine the minimum coverage of the contigs to be clustered, as well as a threshold for the proportion of shared reads in the clustered contigs, thus providing a dynamic range of transcriptome compression that can be adapted according to experimental aims. We compared the performance of Compacta against state of the art clustering algorithms on assemblies from Arabidopsis, mouse and mango, and found that Compacta yielded more rapid results and had competitive precision and recall ratios. We describe and demonstrate a pipeline to tailor Compacta parameters to specific experimental aims.

Conclusions

Compacta is a fast and flexible algorithm for the determination of optimum contig sets that represent the transcriptome for downstream analyses.

Fate of Mycobacterium avium subsp. paratuberculosis and changes in bacterial diversity populations in dairy slurry after chemical treatments

AIMS

A major drawback of using dairy slurry as fertilizer is that it may contains pathogens such as Mycobacterium avium subsp. paratuberculosis (MAP), and it could represent a risk to animal and public health. Thus, the aim of this study was to evaluate the fate of MAP and bacterial communities in dairy slurry after chemical treatments.

METHODS AND RESULTS

Cattle slurry, naturally contaminated with MAP, was collected from a dairy herd and divided into 32 glass bottles which were assigned to eight different treatments (control, 3·0% CaO, 0·5% NaOH; 0·087%, 0·11% and 0·14% H₂ SO₄ ; and 1·0 and 2·5% KMnO₄ ). Treated dairy slurry samples were evaluated at 0, 1, 3, 7, 15, 30 and 60-days following treatment application for viable MAP and dairy slurry pH, and in addition temperature in this material was monitored continuously. Bacterial counts were estimated at each sampling time. A Bayesian zero-inflated Poisson mixed model was fitted to assess the effect of each treatment on the count of MAP cells. Model results indicated that only the 3·0% CaO treatment had a statistically important negative effect on MAP counts during the study period. For most treatments, MAP was undetectable immediately after chemical treatment but re-appeared over time, in some replicates at low concentrations. However, in those cases MAP counts were not statistically different than the control treatment. Regarding the fate of the other bacterial populations, the Firmicutes phylum was the dominant population in the un-treated slurry while Clostridia class members were among the most prevalent bacteria after the application of most chemical treatments.

CONCLUSION

Only 3% CaO treatment had a statistically important negative effect on MAP viability in cattle slurry.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence of MAP partial control in dairy slurry. This information should be considered as a best management practice to reduce MAP and other pathogens for slurry management on dairy farms.

A randomised controlled trial of a program based on the theory of planned behavior to promote fruit and vegetable intake among schoolchildren: PROFRUVE study protocol

BACKGROUND

The PROFRUVE study is a controlled intervention based on the Theory of Planned Behavior (TPB), which follows those behavioral theories that have proved to be the most effective at changing infant fruit and vegetable (FV) intake pattern. The main purpose of the study is to evaluate the effectiveness of an intervention program in increasing FV consumption in schoolchildren aged 8 to 10 and based on TPB.

METHODS

Eligible classrooms within schools from Vitoria-Gasteiz (Basque Country, Spain) will be randomly assigned to the intervention (classrooms n = 4; children n = 86) or control (classrooms n = 4; children n = 86) group. The intervention group will receive 14 sessions of 60 min during an academic year (October to June). These sessions, designed by a multidisciplinary team, are based on TPB and are directed at modifying determinants of behavior (attitudes, subjective norms, perceived behavioral control and intention of consumption), and intake of FV itself. Both the process and the evolution of consumption and determinants of behavior will be evaluated (before, during, shortly after and a year after) using validated surveys, 7 day food records, 24 h reminders and questionnaires.

DISCUSSION

This study will provide a valid and useful tool to achieve changes in the consumption of FV at school level. A negative result will be helpful in redefining new strategies in the framework of changing habits in the consumption of FV.

TRIAL REGISTRATION

This study has been retrospectively registered at ClinicalTrials.gov. Identifier: NCT03400891 . Data registered: 17/01/2018.

On an algorithmic definition for the components of the minimal cell

Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the ‘minimal cell’ and the corresponding ‘minimal genome’, we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed.

An informational view of accession rarity and allele specificity in germplasm banks for management and conservation

Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of diploid, inbred or outbred species.

A decade of the Catalonian Arthroplasty Register (RACat): Variability, exhaustivity, and survival of prostheses between 2005 and 2014

BACKGROUND AND AIM

The Catalonian Arthroplasty Register (RACat) is a public health-based population register used to analyse and evaluate hip and knee replacements in Catalonia. The aim of this study is to present the outcomes after 10 years in operation (January 2005-December 2014).

METHODOLOGY

Using the information from the RACat and the minimum basic data set at hospital discharge, an analysis was made of the quality and exhaustivity of the data, as well as a descriptive analysis of the patients, prostheses, and care process. Survival was also analysed by calculating the accumulated incidence of revisions (according to the cause of intervention in hip replacements and conservation or sacrifice of the posterior cruciate ligament in knee replacement). The relationship between revision risk and the fixation technique of the prosthesis is also analysed, using competitive risk models adjusted for gender, age, and comorbidities.

RESULTS

The main reason for the primary hip and knee replacement surgery was arthrosis. The accumulated incidence of revisions at 10 years was 3.9% in hip replacements caused by arthrosis, and 2.3% in those caused by fracture. Conservation of the posterior cruciate ligament was achieved in 4.4% of knee replacements, with sacrifice in 5.1%.

DISCUSSION

The RACat is consolidated as a tool for the evaluation of joint replacements, with great potential in the analysis of medium and long-term efficacy, the study of the variability in clinical practice, and post-marketing surveillance.

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates

BACKGROUND

Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.

RESULTS

Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome.

CONCLUSIONS

lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

Phosphate starvation induces DNA methylation in the vicinity of cis-acting elements known to regulate the expression of phosphate-responsive genes

Phosphate (Pi) limitation is a constraint for plant growth in many natural and agricultural ecosystems. Plants possess adaptive mechanisms that enable them to cope with conditions of limited Pi supply, including a highly regulated genetic program controlling the expression of genes involved in different metabolic, signaling and development processes of plants. Recently, we showed that in response to phosphate limitation Arabidopsis thaliana sets specific DNA methylation patterns of genic features that often correlated with changes in gene expression. Our findings included, dynamic methylation changes in response to phosphate starvation and the observation that the expression of genes encoding DNA methyltransferases appear to be directly controlled by the key regulator PHOSPHATE RESPONSE 1 (PHR1). These results provide insight into how epigenetic marks can influence plant genomes and transcriptional programs to respond and adapt to harsh conditions. Here we present an analysis of DNA methylation in the upstream regions of low Pi responsive genes in Arabidopsis seedlings exposed to low Pi conditions. We found that hypo- and hyper-methylation in the vicinity of cognate binding sites for transcription factors known to regulate the phosphate starvation response clearly correlates with increased or decreased expression of low-Pi responsive genes.

Cathodoluminescence study of Mg activation in non-polar and semi-polar faces of undoped/Mg-doped GaN core-shell nanorods

Spectrally and spatially resolved cathodoluminescence (CL) measurements were carried out at 80 K on undoped/Mg-doped GaN core-shell nanorods grown by selective area growth metalorganic vapor phase epitaxy in order to investigate locally the optical activity of the Mg dopants. A study of the luminescence emission distribution over the different regions of the nanorods is presented. We have investigated the CL fingerprints of the Mg incorporation into the non-polar lateral prismatic facets and the semi-polar facets of the pyramidal tips. The amount of Mg incorporation/activation was varied by using several Mg/Ga flow ratios and post-growth annealing treatment. For lower Mg/Ga flow ratios, the annealed nanorods clearly display a donor-acceptor pair band emission peaking at 3.26-3.27 eV and up to 4 LO phonon replicas, which can be considered as a reliable indicator of effective p-type Mg doping in the nanorod shell. For higher Mg/Ga flow ratios, a substantial enhancement of the yellow luminescence emission as well as several emission subbands are observed, which suggests an increase of disorder and the presence of defects as a consequence of the excess Mg doping.

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq

RNA-seq experiments estimate the number of genes expressed in a transcriptome as well as their relative frequencies. However, an undetermined number of genes can remain undetected due to their low expression relative to the sample size (sequence depth). Estimation of the true number of genes expressed in a transcriptome is essential in order to determine which genes are exclusively expressed in specific tissues or under particular conditions. A reliable estimate of the true number of expressed genes is also required to accurately measure transcriptome changes and to predict the sequencing depth needed to increase the proportion of detected genes. This problem is analogous to ecological sampling problems such as estimating the number of species at a given site. Here we present a non-parametric estimator for the number of undetected genes as well as for the extra sample size needed to detect a given proportion of the undetected genes. Our estimators are superior to ones already published by having smaller standard errors and biases. We applied our method to a set of 32 publicly available RNA-seq experiments, including the evaluation of 311 individually sequenced libraries. We found that in the majority of the cases more than one thousand genes are undetected, and that on average approximately 6% of the expressed genes per accession remain undetected. This figure increases to approximately 10% if individual sequencing libraries are analyzed. Our method is also applicable to metagenomic experiments. Using our method, the number of undetected genes as well as the sample size needed to detect them can be calculated, leading to more accurate and complete gene expression studies.

Modelling and kinetics studies of a corn-rape blend combustion in an oxy-fuel atmosphere

A kinetic oxy-combustion study of a previously optimized lignocellulose blend is proposed. Kinetic and diffusion control mechanism are considered. The proposed correlations fit properly with the experimental results and diffusion effects are identified as be important enough to be taken into account. Afterwards, with the results obtained in the kinetic study, a detailed consecutive and parallel kinetic scheme is proposed for modelling the oxy-combustion of the blend. A discussion of the temperature and concentration profiles are included. Variation of products final distribution is considered. Smaller particles than 0.001 m are proposed for reducing temperature and concentration profiles and obtaining a good final product distribution. CO2-char reaction is identified as one of the most important step to be optimized for obtaining the lowest final residue. In this study, char is mainly oxidised at 950 K and this situation is attributed to an optimized blending of the bioresidues.

Assessment of stigma associated with tuberculosis in Mexico

BACKGROUND

Stigma is a major barrier to health care access and impacts the quality of life for individuals affected by tuberculosis (TB). Assessing TB stigma is essential to addressing health disparities. However, no such instrument was available in Mexico at the time of our study. This study examined the adaptability of the TB and human immunodeficiency virus (HIV) stigma scales previously used in Thailand.

METHODS

The original scale, developed in English, was linguistically adapted to Spanish and administered to 217 individuals affected by TB in five states in Mexico. The TB-HIV stigma subscales were designed to assess individual and community perspectives. Additional data collected included general information and socio-demographics. Assessment of psychometric properties included basic statistical tests, evaluation of Cronbach's alpha and factor analysis.

RESULTS

We found no significant statistical differences associated with higher stigma scores by location, age, marital status, education and stigma scores. Factor analysis did not create any new factors. Internal consistency reliability coefficients were satisfactory (Cronbach α = 0.876-0.912).

CONCLUSION

The use of the stigma scales has implications for 1) health improvements, 2) research on stigma and health disparities, and 3) TB and HIV stigma interventions. Further research is needed to examine transferability among larger and randomly selected Spanish-speaking populations.

Dynamics of the chili pepper transcriptome during fruit development

BACKGROUND

The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening.

RESULTS

RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueño 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR.

CONCLUSIONS

In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.

Transcriptomic landscape of prophase I sunflower male meiocytes

Meiosis is a form of specialized cell division that generates gametes, allowing recombination of alleles and halving the chromosome number. Arabidopsis and maize are the plant models that have been most extensively studied to determine the genes involved in meiosis. Here we present an RNA-seq study in which gene expression in male meiocytes isolated during prophase I was compared to that in somatic tissues of the sunflower HA89 line. We sampled more than 490 million gene tags from these libraries, assembled them de novo into a sunflower transcriptome. We obtained expression data for 36,304 sunflower genes, of which 19,574 (54%) were differentially expressed (DE) between meiocytes and somatic tissue. We also determined the functional categories and metabolic pathways that are DE in these libraries. As expected, we found large differences between the meiotic and somatic transcriptomes, which is in accordance with previous studies in Arabidopsis and maize. Furthermore, most of the previously implicated meiotic genes were abundantly and DE in meiocytes and a large repertoire of transcription factors (TF) and genes related to silencing are expressed in the sunflower meiocytes. We detected TFs which appear to be exclusively expressed in meiocytes. Our results allow for a better understanding of the conservation and differences in the meiotic transcriptome of plants.

[Quality of life-associated factors at one year after total hip and knee replacement: a multicentre study in Catalonia]

AIMS

To assess the health related quality of life (HRQOL) and associated factors of patients before, and one year after, total knee (TKA) and hip (THA) arthroplasty.

METHODS

A quasi-experimental prospective study conducted in hospitals with different levels of complexity and volume in Catalonia, and on patients with an indication of a TKA or THA. Demographic and psychosocial variables were recorded, and the SF-36 and WOMAC, and a question on perception of change after surgery were administered to patients by telephone interview. The standardised differences (effect size) of perceived change using the SF-36 and WOMAC scores before and after surgery were calculated. The factors associated with HRQOL one year after surgery were analysed using adjusted general linear models.

RESULTS

Although there was an overall improvement in most HRQOL domains of patients (n=672), 9% saw little improvement after surgery, with their scores at baseline and follow-up being very similar (small size effect: 0.0-0.4). Women, patients with low social support, with lower scores (worse) in perceived mental health and baseline HRQOL, and who declared that their condition was more severe, perceived a poorer HRQOL one year after surgery (P<.05).

CONCLUSIONS

Factors associated to a worse prognosis one year after an arthroplasty have been identified and are consistent with other published studies. The assessment of HRQOL can be a key instrument for identifying possible patients without improvement, in order to assess alternatives to an intervention, or apply other interventions in order to improve the efficiency of the healthcare process.

[Arthroplasty registers as post-marketing surveillance systems: the Catalan Arthroplasty Register]

OBJECTIVE

The aim is to present the functioning and results of the Catalan Arthroplasty Registry (RACat).

MATERIAL AND METHOD

The RACat arose by the initiative of the Catalan Society of Orthopaedic Surgery and Traumatology, the Catalan Health Service (CHS) and the Catalan Agency for Health Information Assessment and Quality. Publicly funded hospitals sent information through the Internet (CHS Applications website) on knee and hip arthroplasties: patient identification, hospital, joint (hip/knee), type (primary/revision), side of operation, date of surgery and prosthesis (manufacturer's name and reference number). The quality of the data is analysed regularly. We estimate the risk of replacement by the Kaplan-Meier method.

RESULTS

A total of 52 hospitals out of 62 send data to RACat, and information on 36,951 knee and 26,477 hip arthroplasties is available. Data quality improved between 2005 and 2010. In 2010 coverage exceeded 70%, with side of operation 97%, and prostheses identification of 80%. The risk of replacement at three years was 3.3% (95% CI:3.1-3.6) for knee, 2.9% (95% CI:2.5-3.3) for total hip, and 2.5% (95% CI:2.0-3.1) for partial hip.

DISCUSSION

Risk of replacement is higher than that observed in other registers, although data quality and its improvement over time should be taken into account.

CONCLUSIONS

The information available in the RACat will help to establish a standard that will enable hospitals to compare results.

The capsicum transcriptome DB: a "hot" tool for genomic research

Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/