Consensus Recommendation for Mouse Models of Ocular Hypertension to Study Aqueous Humor Outflow and Its Mechanisms.

Due to their similarities in anatomy, physiology, and pharmacology to humans, mice are a valuable model system to study the generation and mechanisms modulating conventional outflow resistance and thus intraocular pressure. In addition, mouse models are critical for understanding the complex nature of conventional outflow homeostasis and dysfunction that results in ocular hypertension. In this review, we describe a set of minimum acceptable standards for developing, characterizing, and utilizing mouse models of open-angle ocular hypertension. We expect that this set of standard practices will increase scientific rigor when using mouse models and will better enable researchers to replicate and build upon previous findings

Development, characterization and application of novel expressed sequence tag- simple sequence repeat (EST-SSR) markers in radish (Raphanus sativus L.)

In this study, 51,625 unique expressed sequence tag (ESTs) from a total of 289,621 radish ESTs in the National Center for Biotechnology Information (NCBI) database were used to search for simple sequence repeat (SSRs) by SSRLocate, and 2,917 SSRs in 2,891 ESTs were identified. The SSR marker motifs contained di-, tri-, tetra-, penta-, and hexa- nucleotide repeats, and the number was 945 (32.40%), 1,300 (44.57%), 179 (6.14%), 262 (8.98%) and 231 (7.92%), respectively. The motifs AG/CT (16.15%) and GA/TC (13.58%) were the most abundant type. Among 20 amino acids encoded by trinucleotide, Ser (16.17%) was the most common transcript, followed by Leu (13.00%) and Glu (9.90%). A total of 1,082 EST-SSR primers in Raphanus sativus were designed and synthesized, and 864 (79.85%) EST-SSRs were successfully amplified. Polymorphism of these loci was evaluated in a panel of 48 genotypes in Raphanus. The polymorphism information content (PIC) values of those primers varied from 0.33 to 0.84, with a mean value of 0.58. Moreover, it was found that 25 out of 53 EST-SSR primers could be successfully amplified in Brassica species. For its polymorphism, reproducibility and functionality, these novel EST-SSR markers could be used as a powerful tool for marker-assisted selection (MAS) and genetic mapping in radish.Keywords: Raphanus sativus L., expressed sequence tag (EST), simple sequence repeat (SSR), genetic diversity, polymorphism information contentAfrican Journal of Biotechnology Vol. 12(9), pp. 921-93

Transcriptome Profiling of Radish (<i>Raphanus sativus</i> L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

<div><p>Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (<i>Raphanus sativus</i> L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the <i>de novo</i> transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled <i>de novo</i> transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.</p></div

COG function classification of assembled transcripts.

<p>COG function classification of assembled transcripts.</p

The identified genes involved in glutathione metabolism of the <i>de novo</i> transcriptome.

<p>KO (KEGG Orthology), a classification of ortholog and paralog groups based on highly confident sequence similarity scores, and the reaction classification system for biochemical reaction classification, along with other classifications for compounds and drug.</p

Enriched pathways of the up-regulated DEGs.

<p>Enriched pathways of the up-regulated DEGs.</p

Enriched pathways of the down-regulated DEGs.

<p>Enriched pathways of the down-regulated DEGs.</p