Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

<p>Abstract</p> <p>Background</p> <p>Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient and iron deficient conditions.</p> <p>Results</p> <p>Transcriptional profiles of soybean (<it>Glycine max</it>, L. Merr) near isogenic lines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) grown under Fe-sufficient and Fe-limited conditions were analyzed and compared using the Affymetrix^®GeneChip^®Soybean Genome Array. There were 835 candidate genes in the Clark (PI548553) genotype and 200 candidate genes in the IsoClark (PI547430) genotype putatively involved in soybean's iron stress response. Of these candidate genes, fifty-eight genes in the Clark genotype were identified with a genetic location within known iron efficiency QTL and 21 in the IsoClark genotype. The arrays also identified 170 single feature polymorphisms (SFPs) specific to either Clark or IsoClark. A sliding window analysis of the microarray data and the 7X genome assembly coupled with an iterative model of the data showed the candidate genes are clustered in the genome. An analysis of 5' untranslated regions in the promoter of candidate genes identified 11 conserved motifs in 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier, confirming the cluster analysis results.</p> <p>Conclusion</p> <p>These analyses have identified the first genes with expression patterns that are affected by iron stress and are located within QTL specific to iron deficiency stress. The genetic location and promoter motif analysis results support the hypothesis that the differentially expressed genes are co-regulated. The combined results of all analyses lead us to postulate iron inefficiency in soybean is a result of a mutation in a transcription factor(s), which controls the expression of genes required in inducing an iron stress response.</p

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

<p>Abstract</p> <p>Background</p> <p>The GeneChip^®<it>Medicago </it>Genome Array, developed for <it>Medicago truncatula</it>, is a suitable platform for transcript profiling in tetraploid alfalfa [<it>Medicago sativa </it>(L.) subsp. <it>sativa</it>]. However, previous research involving cross-species hybridization (CSH) has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected) and the accuracy of measuring fold-differences in gene expression.</p> <p>Results</p> <p>Transcript profiling using the <it>Medicago </it>GeneChip^®was conducted with elongating stem (ES) and post-elongation stem (PES) internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV) regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs), the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on <it>M. truncatula </it>chromosomes. Clustering simulation analysis of the differentially expressed genes suggested co-expression of some neighbouring genes on <it>Medicago </it>chromosomes.</p> <p>Conclusions</p> <p>The problems associated with transcript profiling in alfalfa stems using the <it>Medicago </it>GeneChip as a CSH platform were mitigated by masking probes targeting ISV regions and SFPs. Using this masking protocol resulted in the identification of numerous candidate genes that may contribute to differences in cell wall concentration and composition of stems of two alfalfa genotypes.</p

AAPT Diagnostic Criteria for Chronic Sickle Cell Disease Pain

Pain in sickle cell disease (SCD) is associated with increased morbidity, mortality, and high health care costs. Although episodic acute pain is the hallmark of this disorder, there is an increasing awareness that chronic pain is part of the pain experience of many older adolescents and adults. A common set of criteria for classifying chronic pain associated with SCD would enhance SCD pain research efforts in epidemiology, pain mechanisms, and clinical trials of pain management interventions, and ultimately improve clinical assessment and management. As part of the collaborative effort between the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks public-private partnership with the U.S. Food and Drug Administration and the American Pain Society, the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks-American Pain Society Pain Taxonomy initiative developed the outline of an optimal diagnostic system for chronic pain conditions. Subsequently, a working group of experts in SCD pain was convened to generate core diagnostic criteria for chronic pain associated with SCD. The working group synthesized available literature to provide evidence for the dimensions of this disease-specific pain taxonomy. A single pain condition labeled chronic SCD pain was derived with 3 modifiers reflecting different clinical features. Future systematic research is needed to evaluate the feasibility, validity, and reliability of these criteria. Perspective: An evidence-based classification system for chronic SCD pain was constructed for the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks-American Pain Society Pain Taxonomy initiative. Applying this taxonomy may improve assessment and management of SCD pain and accelerate research on epidemiology, mechanisms, and treatments for chronic SCD pain

A scoping review of augmented/virtual reality health and wellbeing Interventions for older adults: redefining Immersive virtual reality

Augmented and virtual reality (AR/VR) technologies are regularly used in psychology research to complement psychological interventions and to enable an individual to feel as if they are in an environment other than that of their immediate surroundings. A scoping review was performed to identify how AR/VR was being used with older adult populations to impact their physical and mental health. The review also sought to determine whether the terminology used in AR/VR research was consistent. The results show that 65 studies have been published in the last 20 years that meet the inclusion criteria (virtual/augmented reality) technology to impact older adults’ physical/mental health and wellbeing. Participants included healthy, physically, and cognitively impaired, and emotionally vulnerable older adults. We argue that over 70% of the studies included in this review were mislabeled as VR and only six papers included fully immersive VR/AR. The remaining studies use less immersive variants of virtual reality with their populations, and only one study made use of AR, which prompted the suggestion of a new definition for virtual reality. This paper also calls for an updated taxonomy of augmented and virtual reality definitions to address the lack of consistency found in studies that identify themselves as AR/VR when they are using less immersive technical set-ups, including displaying non-interactive videos on 2D screens

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation.</p> <p>Results</p> <p>The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the <it>Glycine max </it>genome.</p> <p>Conclusions</p> <p>This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of <it>Glycine max </it>can be explored at <url>http://www.soybase.org/soyseq</url>.</p

Gene expression patterns are correlated with genomic and genic structure in soybean

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

Background: The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results: A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions: This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome

“Triple Bottom Line” as “Sustainable Corporate Performance”: A Proposition for the Future

Based upon a review of corporate performance, corporate financial performance and corporate social performance, we propose that the concept of ―triple bottom line‖ (TBL) as ―sustainable corporate performance‖ (SCP) should consist of three measurement elements, namely: (i) financial, (ii) social and (iii) environmental. TBL as SCP is proposed to be derived from the interface between them. We also propose that the content of each of these measurement elements may vary across contexts and over time. Furthermore, TBL as SCR should be interpreted to be a relative concept that is dynamic and iterative. Continuous monitoring needs to be performed, adapting the content of the measurement elements to changes that evolve across contexts and over time in the marketplace and society. TBL as SCP may be seen as a function of time and context. Keywords: triple bottom line; sustainable corporate performance; corporate social performance; financial performanc

Beyond cognitive deficit: the everyday lived experience of dyslexic students at university

This study explores the lived experiences of three dyslexic university students as they negotiate a number of different learning spaces within their higher education institution. The students completed reflective diaries for a period of three weeks and were subsequently interviewed about the experiences they recorded. The transcribed data from the diaries and interviews were analysed using interpretative phenomenological analysis. The following four themes were constructed following analysis: getting things out of my head; holding back – performance as risk; ever-present inner voices – effort of constant self-monitoring; and not belonging in academic spaces – metaphors of misfit. This study argues that attention to the everyday experiences of students with the dyslexia label is as important as knowledge of cognitive differences in the drive to create a more equitable learning environment in higher education