Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p><it>Acacia auriculiformis </it>× <it>Acacia mangium </it>hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in <it>Acacia </it>hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.</p> <p>Results</p> <p>We sequenced transcriptomes of <it>A. auriculiformis </it>and <it>A. mangium </it>from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. <it>De novo </it>assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for <it>A. auriculiformis </it>and <it>A. mangium </it>respectively. The assemblies of <it>A. auriculiformis </it>and <it>A. mangium </it>had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of <it>A. auriculiformis </it>and <it>A. mangium</it>, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection.</p> <p>Conclusion</p> <p>We have produced the first comprehensive transcriptome-wide analysis in <it>A. auriculiformis </it>and <it>A. mangium </it>using <it>de novo </it>assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in <it>Acacia </it>hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.</p

Pre-diagnostic and Diagnostic Stages of Autism Spectrum Disorder: A Parent Perspective

This study examined the experiences of parents receiving an autism spectrum disorder (ASD) diagnosis for their child. Mixed methods were used to give a detailed account of the sequence of events, parents’ experiences and actions associated with the ASD diagnosis. Parents waited nearly two and a half years (mean = 28.72 months) before receiving the ASD diagnosis. Parents with lower general and autism-specific social support, poorer physical health functioning and children with more severe communication problems reported longer wait times. Surprisingly, parents reported more positive than negative experiences from receiving the diagnosis. Paediatricians and psychologists were consulted most frequently; paediatricians and general physicians were rated most likely to neglect early ASD symptoms and least likely to make appropriate referrals. Qualitative analyses revealed seven themes describing the parent experience during the diagnostic process: “heightened awareness”, “initial search”, “dissatisfaction with medical or associated processionals”, “long process/delay”, “feeling uninformed”, “parent psychological and relational experiences” and “diagnosis goals”. A set of commonly experienced stages characterising the process of obtaining a diagnosis were identified and formulated into a six-stage model of diagnostic delay adapted from the patients’ health-seeking model

Cancer Stem Cells in Head and Neck Squamous Cell Carcinoma

Accumulating evidence suggests that self-renewal and differentiation capabilities reside only in a subpopulation of tumor cells, termed cancer stem cells (CSCs), whereas the remaining tumor cell population lacks the ability to initiate tumor development or support continued tumor growth. In head and neck squamous cell carcinoma (HNSCC), as with other malignancies, cancer stem cells have been increasingly shown to have an integral role in tumor initiation, disease progression, metastasis and treatment resistance. In this paper we summarize the current knowledge of the role of CSCs in HNSCC and discuss the therapeutic implications and future directions of this field

Inflammation and Proliferation Act Together to Mediate Intestinal Cell Fusion

Cell fusion between circulating bone marrow-derived cells (BMDCs) and non-hematopoietic cells is well documented in various tissues and has recently been suggested to occur in response to injury. Here we illustrate that inflammation within the intestine enhanced the level of BMDC fusion with intestinal progenitors. To identify important microenvironmental factors mediating intestinal epithelial cell fusion, we performed bone marrow transplantation into mouse models of inflammation and stimulated epithelial proliferation. Interestingly, in a non-injury model or in instances where inflammation was suppressed, an appreciable baseline level of fusion persisted. This suggests that additional mediators of cell fusion exist. A rigorous temporal analysis of early post-transplantation cellular dynamics revealed that GFP-expressing donor cells first trafficked to the intestine coincident with a striking increase in epithelial proliferation, advocating for a required fusogenic state of the host partner. Directly supporting this hypothesis, induction of augmented epithelial proliferation resulted in a significant increase in intestinal cell fusion. Here we report that intestinal inflammation and epithelial proliferation act together to promote cell fusion. While the physiologic impact of cell fusion is not yet known, the increased incidence in an inflammatory and proliferative microenvironment suggests a potential role for cell fusion in mediating the progression of intestinal inflammatory diseases and cancer

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis

Necrotizing enterocolitis (NEC) remains the leading cause of gastrointestinal morbidity and mortality in premature infants. Human and animal studies suggest a role for Paneth cells in NEC pathogenesis. Paneth cells play critical roles in host-microbial interactions and epithelial homeostasis. The ramifications of eliminating Paneth cell function on the immature host-microbial axis remains incomplete. Paneth cell function was depleted in the immature murine intestine using chemical and genetic models, which resulted in intestinal injury consistent with NEC. Paneth cell depletion was confirmed using histology, electron microscopy, flow cytometry, and real time RT-PCR. Cecal samples were analyzed at various time points to determine the effects of Paneth cell depletion with and without Klebsiella gavage on the microbiome. Deficient Paneth cell function induced significant compositional changes in the cecal microbiome with a significant increase in Enterobacteriacae species. Further, the bloom of Enterobacteriaceae species that occurs is phenotypically similar to what is seen in human NEC. This further strengthens our understanding of the importance of Paneth cells to intestinal homeostasis in the immature intestine

Lessons from development: A role for asymmetric stem cell division in cancer

AbstractAsymmetric stem cell division has emerged as a major regulatory mechanism for physiologic control of stem cell numbers. Reinvigoration of the cancer stem cell theory suggests that tumorigenesis may be regulated by maintaining the balance between asymmetric and symmetric cell division. Therefore, mutations affecting this balance could result in aberrant expansion of stem cells. Although a number of molecules have been implicated in regulation of asymmetric stem cell division, here, we highlight known tumor suppressors with established roles in this process. While a subset of these tumor suppressors were originally defined in developmental contexts, recent investigations reveal they are also lost or mutated in human cancers. Mutations in tumor suppressors involved in asymmetric stem cell division provide mechanisms by which cancer stem cells can hyperproliferate and offer an intriguing new focus for understanding cancer biology. Our discussion of this emerging research area derives insight from a frontier area of basic science and links these discoveries to human tumorigenesis. This highlights an important new focus for understanding the mechanism underlying expansion of cancer stem cells in driving tumorigenesis

Science Undergraduates Are Motivated to Undertake Leadership Education to Enhance Employability and Impact

Leadership education is increasingly prevalent, with tertiary institutions offering leadership programs in a variety of formats. Leadership curricula are traditionally underrepresented in science, but provide a promising way to develop a range of transferable skills. Moving forward, it is important for educators and curriculum designers to ask why science students should choose to layer their discipline-specific education with leadership education. Our study aimed to identify the key motivations for undergraduates to choose leadership education alongside a traditional science degree. We surveyed 70 undergraduates across the Bachelor of Science, Bachelor of Science - Advanced Research (Honours) and two emerging science leadership programs (Science Future Leaders and Bachelor of Science Advanced - Global Challenges (Honours)) at Monash University, Australia. We also interviewed 13 students, asking open-ended questions about their motivations for undertaking leadership courses and coded responses to identify common themes. All interviewed students indicated that employability was important in their decision-making. Most respondents were motivated to develop transferable skills and broaden their employment options, competitiveness and adaptability in what scholars have described as an uncertain and dynamic workforce. Some respondents also cited a wish to increase their capacity to have a positive impact in society during their careers. Our findings suggest that today’s Australian science students are receptive to broadening their skills, attributes and competencies beyond traditional technical and content-rich discipline training

Lentiviral-Mediated Transgene Expression Can Potentiate Intestinal Mesenchymal-Epithelial Signaling

Mesenchymal-epithelial signaling is essential for the development of many organs and is often disrupted in disease. In this study, we demonstrate the use of lentiviral-mediated transgene delivery as an effective approach for ectopic transgene expression and an alternative to generation of transgenic animals. One benefit to this approach is that it can be used independently or in conjunction with established transgenic or knockout animals for studying modulation of mesenchymal-epithelial interactions. To display the power of this approach, we explored ectopic expression of a Wnt ligand in the mouse intestinal mesenchyme and demonstrate its functional influence on the adjacent epithelium. Our findings highlight the efficient use of lentiviral-mediated transgene expression for modulating mesenchymal-epithelial interactions in vivo

Isotopes of nitrogen on Mars: Atmospheric measurements by Curiosity's mass spectrometer

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102173/1/wong_readme.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102173/2/wong2013_SM_v4b.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102173/3/grl51166.pd