Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics

<i>C9ORF72</i> repeat expansion causes vulnerability of motor neurons to Ca²⁺-permeable AMPA receptor-mediated excitotoxicity

Funded by The Wellcome Trust (Grant 092742/Z/10/Z), MNDA (Miles/Oct14/878-792), MRC, Euan MacDonald Centre, UK DRI, DBT-India, ISSF (WT/UoE), Royal Society of Edinburgh (CRF), and Biogen/UoE Joint Discovery Research Collaboration. RNA-Seq raw reads were generated by Edinburgh Genomics, The University of Edinburgh. Edinburgh Genomics is partly supported through core grants from NERC (R8/H10/56), MRC (MR/K001744/1), and BBSRC (BB/J004243/1).Mutations in C9ORF72 are the most common cause of familial amyotrophic lateral sclerosis (ALS). Here, through a combination of RNA-seq and electrophysiological studies on induced pluripotent stem cell (iPSC) derived motor neuron (MNs), we show that increased expression of GluA1 AMPA receptor (AMPAR) subunit occurs in MNs with C9ORF72 mutations that leads to increased Ca2+-permeable AMPAR expression and results in enhanced selective MN vulnerability to excitotoxicity. These deficits are not found in iPSC-derived cortical neurons and are abolished by CRISPR/Cas9-mediated correction of the C9ORF72 repeat expansion in MNs. We also demonstrate that MN-specific dysregulation of AMPAR expression is also present in C9ORF72 patient post mortem material. We therefore present multiple lines of evidence for the specific upregulation of GluA1 subunits in human mutant C9ORF72 MNs that could lead to a potential pathogenic excitotoxic mechanism in ALS.Publisher PDFPeer reviewe

Track E Implementation Science, Health Systems and Economics

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138412/1/jia218443.pd

To investigate the potential of Moringa oleifera leaf extract and broccoli (Brassica oleracea) leaf extract as Sodium sulphite replacers in preserving minced meat

Minced meat is a nutritionally dense and highly perishable food, therefore there is need for preserving it. Most artificial preservatives currently used to prevent food spoilage have been reported to cause various health problems hence the need to use natural preservatives. Moringa oleifera and Brassica oleracea (broccoli) leaf extracts have proved their potential to be used as natural preservatives. The main objective of this research was to determine the antimicrobial efficacy of Moringa oleifera and broccoli leaf extracts as minced meat preservatives. Seven minced meat samples were prepared with different preservative concentrations. The first one had no preservative, the second one was preserved with 0.1% sodium sulphite, the third one was preserved with 1% Moringa oleifera leaf extract, the fourth one was preserved with 2% Moringa oleifera leaf extract, the fifth one was preserved with 1% broccoli leaf extract, the sixth one was preserved with 2% broccoli leaf extract and the seventh one was preserved with 1% Moringa oleifera and 1% broccoli leaf extracts. The minced meat samples were tested periodically (after 1, 12, 24, 48 and 72 hours) for microbial load (Total Bacterial Count, Coliforms, Salmonella, Escherichia coli and Staphylococcus aureus), colour stability and sensory analysis. Escherichia coli and Salmonella were not detected in all samples. The Total Bacteria, Staphylococcus aureus and Coliform counts for the samples varied from 4.3- 5.98 log CFU/gram, 1.32- 3.91 log CFU/gram and 3.4- 5.3 log CFU/gram respectively. The colour a*, L* and b*- values had ranges between 5-14, 53.2- 44.2 and 12- 15 respectively. The differences were compared using Graph pad prism 4 one way ANOVA for significant difference (α 0.05). It was concluded that there was no significant difference in the shelf life of the minced meat preserved with broccoli and Moringa oleifera leaf extracts to the one preserved with sodium sulphite

An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin

Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin mutant (R36S) shows no post-translational modifications. After aging for nine months in the absence of light, a thiol-adduct (dithiothreitol) modifying surface cysteines is observed by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system