An Intronic microRNA Links Rb/E2F and EGFR Signaling

The importance of microRNAs in the regulation of various aspects of biology and disease is well recognized. However, what remains largely unappreciated is that a significant number of miRNAs are embedded within and are often co-expressed with protein-coding host genes. Such a configuration raises the possibility of a functional interaction between a miRNA and the gene it resides in. This is exemplified by the Drosophila melanogaster dE2f1 gene that harbors two miRNAs, mir-11 and mir-998, within its last intron. miR-11 was demonstrated to limit the proapoptotic function of dE2F1 by repressing cell death genes that are directly regulated by dE2F1, however the biological role of miR-998 was unknown. Here we show that one of the functions of miR-998 is to suppress dE2F1-dependent cell death specifically in rbf mutants by elevating EGFR signaling. Mechanistically, miR-998 operates by repressing dCbl, a negative regulator of EGFR signaling. Significantly, dCbl is a critical target of miR-998 since dCbl phenocopies the effects of miR-998 on dE2f1-dependent apoptosis in rbf mutants. Importantly, this regulation is conserved, as the miR-998 seed family member miR-29 repressed c-Cbl, and enhanced MAPK activity and wound healing in mammalian cells. Therefore, the two intronic miRNAs embedded in the dE2f1 gene limit the apoptotic function of dE2f1, but operate in different contexts and act through distinct mechanisms. These results also illustrate that examining an intronic miRNA in the context of its host''s function can be valuable in elucidating the biological function of the miRNA, and provide new information about the regulation of the host gene itself.     

水稻盐胁迫相关内含子microRNA的表达及其生物发生机制

内含子microRNA是一类位于编码基因内含子区域的非编码小RNA。目前,动物内含子microRNA研究报道较多,而关于植物体内含子microRNA的功能及其生物发生机制报道较少。本研究通过高通量测序技术,结合生物信息学方法,发现在盐胁迫条件下水稻幼苗中共85个内含子microRNAs表达,其中差异表达的有24个。预测到的51个靶基因的功能分析,主要涉及抗氧化途径、植物激素信号转导途径及功能基因表达调控途径。此外,根据宿主基因的表达情况推测,共30个内含子microRNAs具有独立表达的功能。通过分析内含子microRNA前体DNA片段上游1 kb序列中的启动子核心元件,初步验证其具有独立表达的能力。因此,推测水稻幼苗在盐胁迫条件下,部分内含子microRNA独立于宿主基因表达,并参与水稻盐胁迫下的自我防御机制。     

microRNA计算发现方法的研究进展

microRNA (miRNA)是近几年发现的一类长度为～21 nt的内源非编码小RNA, 在植物和动物中发挥着重要而广泛的调控功能。它的发现主要有cDNA克隆测序和计算发现两条途径。由于cDNA克隆测序方法受miRNA表达的时间和组织特异性以及表达水平的影响, 而计算发现可以弥补其不足, 因此miRNA的计算发现方法研究受到了广泛的重视。文章对近几年计算发现miRNA的研究进展进行了综述, 根据计算发现方法的本质, 将计算发现方法归纳为5类, 分别是同源片段搜索方法、基于比较基因组学的预测方法、基于序列和结构特征打分的预测方法、结合作用靶标的预测方法和基于机器学习的预测方法, 并对各类方法的原理、核心思想、优点和局限性进行了分析, 最后探讨了进一步的发展方向。     

Sweating the small stuff: microRNA discovery in plants

The class of small RNAs known as microRNAs (miRNAs) has a demonstrated role in the negative regulation of gene expression in both plants and animals. These small molecules have been shown to play a critical role in a wide range of developmental and physiological pathways. Although hundreds of different miRNAs have now been identified using cloning and computational approaches, characterization of their targets and biological roles has been more limited. New sequencing technologies promise to accelerate the sequencing of small RNAs and additional genetic and genomic strategies are being applied to assess their regulatory function on RNA targets. These technologies will enable the identification of large numbers of small RNAs from diverse species, and comparative genomics approaches based on these data are likely to identify additional miRNAs. Combined with bioinformatics and experimental approaches to separate miRNAs from short-interfering RNAs (siRNAs), the pace of miRNA discovery is likely to accelerate, leading to an improved understanding of miRNA function and biological significance.     

Combinatorial libraries and biological discovery

Combinatorial chemistry has become a popular tool for the preparation of collections of compounds that can be used to find inhibitors and substrates for different protein targets. It has evolved to provide small molecule libraries, which, with the concomittant use of affinity chromatography, gene expression profiling and complementation, can be used to identify compounds and their protein targets in biological systems, including the neurological system.     

Hyaluronic acid: separation and biological implications

Hyaluronic acid (hyaluronan) is a ubiquitous extracellular matrix component, and present at high concentrations in skin, joints and cornea. In the skin, it is synthesized primarily by dermal fibroblasts and by epidermal keratinocytes. Hyaluronic acid usually exists as a high molecular mass (600,000-1,000,000) and non-sulfated glycosaminoglycan composed of a disaccharide unit of [bond]3GlcNAc beta 1[bond]4GlcA beta 1[bond]. Hyaluronic acid has been widely used not only for osteoarthritis and ophthalmology but also for cosmetics for skin care. To examine the biological activities of hyaluronic acid, we have to accurately determine the quantity and molecular masses in biological samples. We review recent development in the analysis of hyaluronic acid having various molecular sizes using electrophoretic and chromatographic techniques. Recently, interactions between hyaluronic acid oligomers and hyaluronic acid-binding proteins have attracted the interest for understanding the biological functions. We show some interesting reports on biological interactions of hyaluronic acid and its oligomers with some proteins.     

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

In recent years, microRNAs have been shown to play important roles in physiological as well as malignant processes. The PhenomiR database provides data from 542 studies that investigate deregulation of microRNA expression in diseases and biological processes as a systematic, manually curated resource. Using the PhenomiR dataset, we could demonstrate that, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies.     

Biomarker discovery in biological fluids

Discovery of novel protein biomarkers is essential for successful drug discovery and development. These novel protein biomarkers may aid accelerated drug efficacy, response, or toxicity decision making based on their enhanced sensitivity and/or specificity. These biomarkers, if necessary, could eventually be converted into novel diagnostic marker assays. Proteomic platforms developed over the past few years have given us the ability to rapidly identify novel protein biomarkers in various biological matrices from cell cultures (lysates, supernatants) to human clinical samples (serum, plasma, and urine). In this article, we delineate an approach to biomarker discovery. This approach is divided into three steps, (i) identification of markers, (ii) prioritization of identified markers, and (iii) preliminary validation (qualification) of prioritized markers. Using drug-induced idiosyncratic hepatotoxicity as a case study, the article elaborates methods and techniques utilized during the three steps of biomarker discovery process. The first step involves identification of markers using multi-dimensional protein identification technology. The second step involves prioritization of a subset of marker candidates based on several criteria such as availability of reagent set for assay development and literature association to disease biology. The last step of biomarker discovery involves development of preliminary assays to confirm the bio-analytical measurements from the first step, as well as qualify the marker(s) in pre-clinical models, to initiate future marker validation and development.     

Cell-selective proteomics for biological discovery

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Interleukin-18: biological properties and clinical implications

IL-18, originally identified as interferon-gamma inducing factor (IGIF), is related to the IL-1 family in terms of its structure, processing, receptor, signal transduction pathway and pro-inflammatory properties. IL-18 is also functionally related to IL-12, as it induces the production of Th1 cytokines and participates in cell-mediated immune cytotoxicity. This review summarizes the recent advances in the understanding of IL-18 structure, processing, receptor expression and immunoregulatory functions, and focuses on the role of IL-18 modulation in tumours, infections, and autoimmune and inflammatory diseases.     

IL-20: biological functions and clinical implications

Summary IL-20 belongs to the IL-10 family and plays a role in skin inflammation and the development of hematopoietic cells. Little is known about its other biological functions and clinical implications, however. Updated information about IL-20, such as its identification, expression, receptors, signaling, biological activities, and potential clinical implications, is illustrated in this review based on our research and on data available in the literature. Our studies of IL-20 show that it is a pleiotropic cytokine with potent inflammatory, angiogenic, and chemoattractive characteristics. Inflammation and angiogenesis are essential for the pathogenesis of rheumatoid arthritis and atherosclerosis. Based on in vitro data and clinical samples, we demonstrated that IL-20 is involved in the diseases of rheumatoid arthritis and atherosclerosis. In addition, we found in our studies that IL-20 signaled through different molecules in several cells. The present review presents the clinical implications of IL-20 in rheumatoid arthritis and atherosclerosis. It may provide new therapeutic options in the future.This work was supported by a grant from Chi-Mei Medical Center, Tainan, Taiwan.     

Antibiotic resistance is ancient: implications for drug discovery

An unfailing observation over the past 70 years is that resistance to all antibiotics emerges eventually after use in the clinic. Where does this resistance come from? Recent work has shown that antibiotic resistance genes are common in metagenomes of ancient sediments. This prevalence of resistance, well before the use of antibiotics, denotes the importance of taking microbial chemical ecology and deep metagenomic profiling into account in the development and use of antibiotics.     

GPDE: A biological proteomic database for biomarker discovery and evaluation

Clinical proteomics faces extremely complex and variable data. Here, we present an updated version of the Griss Proteomics Database Engine (GPDE): A free biological proteomic database specifically designed for clinical proteomics and biomarker discovery (http://gpde.sourceforge.net). It combines experiments based on investigated cell types thereby supporting customizable biological meta-analyses. Through the new features described here, the GPDE now became a powerful yet easy-to-use tool to support the fast identification and reliable evaluation of biomarker candidates.     

Biomarker discovery: proteome fractionation and separation in biological samples.

Proteomics, analogous with genomics, is the analysis of the protein complement present in a cell, organ, or organism at any given time. While the genome provides information about the theoretical status of the cellular proteins, the proteome describes the actual content, which ultimately determines the phenotype. The broad application of proteomic technologies in basic science and clinical medicine has the potential to accelerate our understanding of the molecular mechanisms underlying disease and may facilitate the discovery of new drug targets and diagnostic disease markers. Proteomics is a rapidly developing and changing scientific discipline, and the last 5 yr have seen major advances in the underlying techniques as well as expansion into new applications. Core technologies for the separation of proteins and/or peptides are one- and two-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography, and these are coupled almost exclusively with mass spectrometry. Proteomic studies have shown that the most effective analysis of even simple biological samples requires subfractionation and/or enrichment before protein identification by mass spectrometry. Selection of the appropriate technology or combination of technologies to match the biological questions is essential for maximum coverage of the selected subproteome and to ensure both the full interpretation and the downstream utility of the data. In this review, we describe the current technologies for proteome fractionation and separation of biological samples, based on our lab workflow for biomarker discovery and validation.     

Total synthesis of isoprostanes: discovery and quantitation in biological systems

Isoprostanes (iP's), a new class of natural products isomeric with prostaglandins, are formed as the result of free radical oxygenation of polyunsaturated fatty acids. We have identified these iP's and developed analytical methodology to measure them in biological fluids. The approach we took, which led to the discovery and measurement of iP's, is as follows: (1) based on some biochemical and chemical considerations, we proposed possible structures for these isoprostanes; (2) we performed the total syntheses of some of these iP's, in particular Groups III through VI, and used them as markers for their discovery in biological fluids and developed a GC/MS and an LC/MS methodologies based on iPF2alpha-III, iPF2alpha-VI, and 8,12-iso-iPF2alpha-VI; (3) with the help of these assays, we measured elevated levels of iP's in Alzheimer's disease and atherosclerosis.     

Illuminating drug discovery with biological pathways

Systems biology promises to impact significantly on the drug discovery process. One of its ultimate goals is to provide an understanding of the complete set of molecular mechanisms describing an organism. Although this goal is a long way off, many useful insights can already come from currently available information and technology. One of the biggest challenges in drug discovery today is the high attrition rate: many promising candidates prove ineffective or toxic owing to a poor understanding of the molecular mechanisms of biological systems they target. A "systems" approach can help identify pathways related to a disease and can suggest secondary effects of drugs that might cause these problems and thus ultimately improve the drug discovery pipeline.