A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)

<p>Abstract</p> <p>Background</p> <p>Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time of this writing). To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available ESTs database. Matching sequences have then been related to Unigene clusters on which most of this study was based.</p> <p>Results</p> <p>One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of <it>Triticum </it>are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found.</p> <p>Conclusions</p> <p>This study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.</p

In Vitro vs In Silico Detected SNPs for the Development of a Genotyping Array: What Can We Learn from a Non-Model Species?

Background: There is considerable interest in the high-throughput discovery and genotyping of single nucleotide polymorphisms (SNPs) to accelerate genetic mapping and enable association studies. This study provides an assessment of EST-derived and resequencing-derived SNP quality in maritime pine (Pinus pinaster Ait.), a conifer characterized by a huge genome size (~23.8 Gb/C). [br/] Methodology/Principal Findings: A 384-SNPs GoldenGate genotyping array was built from i/ 184 SNPs originally detected in a set of 40 re-sequenced candidate genes (in vitro SNPs), chosen on the basis of functionality scores, presence of neighboring polymorphisms, minor allele frequencies and linkage disequilibrium and ii/ 200 SNPs screened from ESTs (in silico SNPs) selected based on the number of ESTs used for SNP detection, the SNP minor allele frequency and the quality of SNP flanking sequences. The global success rate of the assay was 66.9%, and a conversion rate (considering only polymorphic SNPs) of 51% was achieved. In vitro SNPs showed significantly higher genotyping-success and conversion rates than in silico SNPs (+11.5% and +18.5%, respectively). The reproducibility was 100%, and the genotyping error rate very low (0.54%, dropping down to 0.06% when removing four SNPs showing elevated error rates). [br/] Conclusions/Significance: This study demonstrates that ESTs provide a resource for SNP identification in non-model species, which do not require any additional bench work and little bio-informatics analysis. However, the time and cost benefits of in silico SNPs are counterbalanced by a lower conversion rate than in vitro SNPs. This drawback is acceptable for population-based experiments, but could be dramatic in experiments involving samples from narrow genetic backgrounds. In addition, we showed that both the visual inspection of genotyping clusters and the estimation of a per SNP error rate should help identify markers that are not suitable to the GoldenGate technology in species characterized by a large and complex genome

Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

<p>Abstract</p> <p>Background</p> <p>Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on traits important to producers and consumers, including those associated with growth, nutrition, reproduction, immune response, and fillet quality. Understanding and monitoring the biological mechanisms underlying stress responses will facilitate alleviating their negative effects through selective breeding and changes in management practices, resulting in improved animal welfare and production efficiency.</p> <p>Results</p> <p>Physiological responses to five treatments associated with stress were characterized by measuring plasma lysozyme activity, glucose, lactate, chloride, and cortisol concentrations, in addition to stress-associated transcripts by quantitative PCR. Results indicate that the fish had significant stressor-specific changes in their physiological conditions. Sequencing of a pooled normalized transcriptome library created from gill, brain, liver, spleen, kidney and muscle RNA of control and stressed fish produced 3,160,306 expressed sequence tags which were assembled and annotated. SNP discovery resulted in identification of ~58,000 putative single nucleotide polymorphisms including 24,479 which were predicted to fall within exons. Of these, 4907 were predicted to occupy the first position of a codon and 4110 the second, increasing the probability to impact amino acid sequence variation and potentially gene function.</p> <p>Conclusion</p> <p>We have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments. This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species.</p

The Influence of Manga on the Graphic Novel

This material has been published in The Cambridge History of the Graphic Novel edited by Jan Baetens, Hugo Frey, Stephen E. Tabachnick. This version is free to view and download for personal use only. Not for re-distribution, re-sale or use in derivative works. © Cambridge University PressProviding a range of cogent examples, this chapter describes the influences of the Manga genre of comics strip on the Graphic Novel genre, over the last 35 years, considering the functions of domestication, foreignisation and transmedia on readers, markets and forms

House Rules: A Novel

When your son can’t look you in the eye…does that mean he’s guilty? Jacob Hunt is a teen with Asperger’s syndrome. He’s hopeless at reading social cues or expressing himself well to others, though he is brilliant in many ways. He has a special focus on one subject—forensic analysis. A police scanner in his room clues him in to crime scenes, and he’s always showing up and telling the cops what to do. And he’s usually right. But when Jacob’s small hometown is rocked by a terrible murder, law enforcement comes to him. Jacob’s behaviors are hallmark Asperger’s, but they look a lot like guilt to the local police. Suddenly the Hunt family, who only want to fit in, are thrust directly in the spotlight. For Jacob’s mother, it’s a brutal reminder of the intolerance and misunderstanding that always threaten her family. For his brother, it’s another indication why nothing is normal because of Jacob. And for the frightened small town, the soul-searing question looms: Did Jacob commit murder? House Rules is “a provocative story in which [Picoult] explores the pain of trying to comprehend the people we love—and reminds us that the truth often travels in disguise” (People).https://scholarship.law.ua.edu/harper_lee_prize_books_2011/1019/thumbnail.jp

Effets potentiels de la grande vitesse régionale sur la cohérence territoriale : modélisation de services régionaux à grande vitesse et évaluation par mesures d’accessibilité dans la région Grand Est

The modification of the perimeter of the French regions as part of the last territorial reform of 2015 leads to enlist the concept of territorial coherence. In the Greater East region, territorial practices and spatial representations have not changed despite the need to bring out a common living area. The Greater East region remains marked by the juxtaposition of three entities (Alsace, Lorraine, Champagne-Ardenne), each of them operating with a specific dynamic.The networking of these entities represents a means of ensuring a transversal functioning, which could be a vector for a greater use of the regional railway network. This networking can be carried out by the rail network itself: one of the main instruments of territorial coherence through its dual capacity to support mobility and to condition their emergence.Faced with the limitations of the conventional network to meet the challenges of travel on the scale of an enlarged region, the high-speed network reserves opportunities for optimization through the deployment of regional high-speed services. A decision-support tool is developed in order to highlight the improvements of the network and the rail services needed to meet these challenges. An approach by the schedule accessibility of the territories which considers the train schedules will enable the modelling of scenarios previously defined within a prospective approach.La modification du périmètre des régions dans le cadre de la réforme territoriale de 2015 conduit à mobiliser le concept de cohérence territoriale. En effet, dans la région Grand Est, les pratiques territoriales et les représentations spatiales n’ont pas évolué malgré la nécessité de faire émerger un territoire de vie commun. La région reste ainsi marquée par la mitoyenneté de trois ensembles (Alsace, Lorraine, Champagne-Ardenne) fonctionnant selon une dynamique propre à chacun. La mise en réseau de ces entités représente un moyen d’assurer un fonctionnement transversal plus cohérent et vecteur d’un usage plus important du réseau ferré régional. Cette mise en réseau peut être portée par le réseau ferré lui-même, un des principaux instruments de cohérence territoriale à travers sa double capacité à supporter les mobilités et à conditionner leur émergence. Face aux limites que présente le réseau classique pour répondre aux enjeux de déplacements à l’échelle d’une région élargie, le réseau à grande vitesse réserve quant à lui des opportunités d’optimisation à travers le déploiement de services régionaux à grande vitesse. Un outil d’aide à la décision est développé afin d’étudier les évolutions du réseau et des services ferroviaires permettant de répondre à ces enjeux. Une approche par l’accessibilité horaire des territoires a pour but la simulation de scénarios préalablement définis dans un volet prospectif

Small great things: a novel

This stunning new novel is Jodi Picoult at her finest--complete with unflinching insights, richly layered characters, and a page-turning plot with a gripping moral dilemma at its heart. Ruth Jefferson is a labor and delivery nurse at a Connecticut hospital with more than twenty years\u27 experience. During her shift, Ruth begins a routine checkup on a newborn, only to be told a few minutes later that she\u27s been reassigned to another patient. The parents are white supremacists and don\u27t want Ruth, who is African American, to touch their child. The hospital complies with their request, but the next day, the baby goes into cardiac distress while Ruth is alone in the nursery. Does she obey orders or does she intervene? Ruth hesitates before performing CPR and, as a result, is charged with a serious crime. Kennedy McQuarrie, a white public defender, takes her case but gives unexpected advice: Kennedy insists that mentioning race in the courtroom is not a winning strategy. Conflicted by Kennedy\u27s counsel, Ruth tries to keep life as normal as possible for her family--especially her teenage son--as the case becomes a media sensation. As the trial moves forward, Ruth and Kennedy must gain each other\u27s trust, and come to see that what they\u27ve been taught their whole lives about others--and themselves--might be wrong. With incredible empathy, intelligence, and candor, Jodi Picoult tackles race, privilege, prejudice, justice, and compassion--and doesn\u27t offer easy answers. Small Great Things is a remarkable achievement from a writer at the top of her game. Praise for Jodi Picoult\u27s Leaving Time A riveting drama. --Us Weekly [A] moving tale. --People A fast-paced, surprise-ending mystery. --USA Today Poignant. an entertaining story about parental love, friendship, loss. --The Washington Post -- Provided by publisher; A woman and her husband admitted to a hospital to have a baby requests that their nurse be reassigned - they are white supremacists and don\u27t want Ruth, who is black, to touch their baby. The hospital complies, but the baby later goes into cardiac distress when Ruth is on duty. She hesitates before rushing in to perform CPR. When her indecision ends in tragedy, Ruth finds herself on trial, represented by a white public defender who warns against bringing race into a courtroom. As the two come to develop a truer understanding of each other\u27s lives, they begin to doubt the beliefs they each hold most dear -- Provided by publisher ; Includes bibliographical references (pages 469-470) ; New York Times Best Seller Listhttps://scholarship.law.ua.edu/harper_lee_prize_books_2017/1020/thumbnail.jp

House Rules: A Novel

When your son can’t look you in the eye…does that mean he’s guilty? Jacob Hunt is a teen with Asperger’s syndrome. He’s hopeless at reading social cues or expressing himself well to others, though he is brilliant in many ways. He has a special focus on one subject—forensic analysis. A police scanner in his room clues him in to crime scenes, and he’s always showing up and telling the cops what to do. And he’s usually right. But when Jacob’s small hometown is rocked by a terrible murder, law enforcement comes to him. Jacob’s behaviors are hallmark Asperger’s, but they look a lot like guilt to the local police. Suddenly the Hunt family, who only want to fit in, are thrust directly in the spotlight. For Jacob’s mother, it’s a brutal reminder of the intolerance and misunderstanding that always threaten her family. For his brother, it’s another indication why nothing is normal because of Jacob. And for the frightened small town, the soul-searing question looms: Did Jacob commit murder? House Rules is “a provocative story in which [Picoult] explores the pain of trying to comprehend the people we love—and reminds us that the truth often travels in disguise” (People).https://scholarship.law.ua.edu/harper_lee_prize_books_2011/1019/thumbnail.jp