Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements

Background: Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms they are reported to play a role in cellular differentiation and development. They show an enriched expression in the brain where they are implicated in maintaining cellular identity, homeostasis, stress responses and plasticity. Low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncRNAs in other vertebrates. A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.Results: Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. Using ROC analyses we were able to define a measure to select significantly conserved lncRNAs. Indeed, starting from ~2,800 mouse lncRNAs we could predict that between 4 and 11% present conserved sequence fragments in fish genomes. Gene ontology (GO) enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar GO classes like regulation of transcription and central nervous system development. The proximal coding genes in both the species show enrichment of their expression in brain. In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.Conclusions: Conservation at the sequence level can identify a subset of putative lncRNA orthologs. The similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. The pipeline herein presented represents a proof of principle showing that a portion between 4 and 11% of lncRNAs retains region of conservation between mammals and fishes. We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes. \uc2\ua9 2013 Basu et al.; licensee BioMed Central Ltd

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

Genome-wide expression analysis using next generation sequencing (RNA-Seq) provides an opportunity for in-depth molecular profiling of fundamental biological processes, such as cellular differentiation and malignant transformation. Differentiating human neurons derived from induced pluripotent stem cells (iPSCs) provide an ideal system for RNA-Seq since defective neurogenesis caused by abnormalities in transcription factors, DNA methylation, and chromatin modifiers lie at the heart of some neuropsychiatric disorders. As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients

Plant productivity is a key driver of soil respiration response to climate change in a nutrient-limited soil

Despite knowledge of the interaction between climate change factors significant uncertainty exists concerning the individual and interactive effects of elevated carbon dioxide (eCO2) and elevated temperature (eT) on the soil microbiome and function. Here we examine the individual and interactive effects of eCO2 and eT on tree growth, soil respiration (Rsoil), biomass, structural and functional composition of microbial community, nitrogen (N) mineralisation and N availability in a whole tree chamber experiment. Eucalyptus globulus plants were grown from seedling to ca. 10 m tall for 15 months in a nutrient-poor sandy soil under ambient and elevated (+ 240 ppm) atmospheric CO2 concentrations combined with ambient or elevated temperatures (+ 3 °C) in a full factorial design. Plant growth was strongly stimulated under eCO2, but eT had little impact on any measured plant property. In contrast, Rsoil was not consistently affected by eCO2 or eT, but correlated strongly with root and leaf biomass. The response of N-mineralisation and nutrient availability to eCO2 and eT varied across time, and available N correlated strongly with plant height. Further, the C:N ratio of the microbial biomass and leaves were both higher under eCeT treatment. However, these functional measures were not significantly linked to either structural or functional diversity of the soil microbiome. Taken together, these results suggest that in this low-nutrient soil, belowground processes are principally driven by aboveground productivity. Our work provides novel insight into mechanisms underlying above- and belowground response to climate change, and the potential to sequester C in a low-nutrient status soil under future climatic conditions may be limited

Teaching boys and gender justice

This paper explores issues in the teaching of boys within a gender just framework. It identifies the productive pedagogies model as an appropriate means by which the specifics of boys' education can be considered. It avoids essentialist accounts of boys' pedagogies to suggest that pedagogies directed towards boys have to foreground issues of gender justice and privilege. There is a recognition that schools do not meet the needs of some boys. However, there is also a recognition that schools do not meet the needs of many girls and that some boys are a problem for girls and teachers as well as each other. Hence, this paper suggests ways in which pedagogies directed towards the specifics of boys' education can improve the educational experiences of girls, boys and teachers. In the process it also notes some of the dangers of a take up of the productive pedagogies model with boys without a demonstrated commitment to gender justice

Community composition based on pyrosequencing.

<p>The relative abundance of each microbial phylum (Archaea, n = 1; Bacteria, n = 13; Fungi, n = 4) is indicated for precooling (pc), control and cooled treatments.</p

Microbial biomass estimated using a) SIR, b) CFE and c) qPCR methods and corrected for carbon loss in the control treatment (interpolated between pre-cooling and control treatment end of experiment biomasses, so that the MAT plus 3°C soils were compared to the cooled (MAT minus 3°C) soils at a similar C loss, corresponding to the maximum C loss of cooled samples at the end of the experiment.

<p>Each soil is identified by geographic/climatic area including 1 (subarctic), 2 (Scotland), 3 (England), 4 (Mediterranean) and 5 (tropical), and ecosystem type: A (arable), C (coniferous evergreen forest), D (deciduous broadleaf forest), G (grassland), H (ericaceous heath) and E (evergreen broadleaf forest) (21). Mean ± S.E. is presented (n = 3). Black bars (control treatment), grey bars (cooled treatment). Statistically significant differences (<i>P</i><0.05) are marked with an asterisk.</p

Authorities who issued the permission for soil sampling.

<p>Authorities who issued the permission for soil sampling.</p