Characterization of microRNA expression profiles in normal human tissues

<p>Abstract</p> <p>Background</p> <p>Measuring the quantity of miRNAs in tissues of different physiological and pathological conditions is an important first step to investigate the functions of miRNAs. Matched samples from normal state can provide essential baseline references to analyze the variation of miRNA abundance.</p> <p>Results</p> <p>We provided expression data of 345 miRNAs in 40 normal human tissues, which identified universally expressed miRNAs, and several groups of miRNAs expressed exclusively or preferentially in certain tissue types. Many miRNAs with co-regulated expression patterns are located within the same genomic clusters, and candidate transcriptional factors that control the pattern of their expression may be identified by a comparative genomic strategy. Hierarchical clustering of normal tissues by their miRNA expression profiles basically followed the structure, anatomical locations, and physiological functions of the organs, suggesting that functions of a miRNA could be appreciated by linking to the biologies of the tissues in which it is uniquely expressed. Many predicted target genes of miRNAs that had specific reduced expression in brain and peripheral blood mononuclear cells are required for embryonic development of the nervous and hematopoietic systems based on database search.</p> <p>Conclusion</p> <p>We presented a global view of tissue distribution of miRNAs in relation to their chromosomal locations and genomic structures. We also described evidence from the <it>cis</it>-regulatory elements and the predicted target genes of miRNAs to support their tissue-specific functional roles to regulate the physiologies of the normal tissues in which they are expressed.</p

Bulk dense fine-grain (1-x)BiScO\u3csub\u3e3\u3c/sub\u3e–xPbTiO\u3csub\u3e3\u3c/sub\u3e ceramics with high piezoelectric coefficient

High density fine grain (1−x)BiScO3–xPbTiO3 ceramics were successfully prepared by two-step sintering and their ferroelectric properties were investigated. Experimental evidence indicates the existence of a morphotropic phase boundary at the composition zx=0.635, which exhibits a piezoelectric coefficient d33 of 700 pC/N at room temperature, significantly higher than the reported values to date. Furthermore, a higher electromechanical coupling factor Kp=0.632 and a larger remnant polarization Pr=47.3 µC/cm2 were obtained. The paraelectric-to-ferroelectric phase transition occurs at 446 °C, slightly lower than in the coarse grain ceramics with a similar composition, suggesting a grain size effect. The local effective piezoelectric coefficient d33* was estimated to be 795 pC/N at 2.29 V, measured by scanning probe microscopy. Further atomic force microscope observation revealed the existence of 90° domains of about 60–70 nm in width, confirming the previous results that small domain structure enhances the piezoelectric properties

Development or absence of conjugate fractures in low-permeability sandstones

Natural fractures are ubiquitous in rocks. The Coulomb law of Mohr’s failure theory predicts that the angle between conjugate failure surfaces is a constant. In the Ordos Basin, observing the development of two groups of conjugate fractures in the field, cores and imaging logging is very difficult. In this paper, the directions of paleocurrents in the Upper Triassic Yanchang Formation of the Ordos Basin are determined by measuring the orientations of field bedding. Through the correlation analysis of paleocurrent and natural fracture orientations, when the sediment comes from a single source, a group of fractures with a large angle between conjugate fractures and the paleocurrent direction is found not to develop. When the sediments in the study area have two provenances, both provenance directions affect the development of conjugate fractures. In the southern Ordos Basin, influenced by the direction of paleocurrent flow in the near-north direction, fractures in the near N‒S direction develop. Through rock mechanics experiments in different directions, the planar anisotropy in rock mechanics parameters caused by the direction of paleocurrent flow is found to be the geological factor leading to various degrees of fracture development in different directions within the Ordos Basin

The microRNA body map : dissecting microRNA function through integrative genomics

While a growing body of evidence implicates regulatory miRNA modules in various aspects of human disease and development, insights into specific miRNA function remain limited. Here, we present an innovative approach to elucidate tissue-specific miRNA functions that goes beyond miRNA target prediction and expression correlation. This approach is based on a multi-level integration of corresponding miRNA and mRNA gene expression levels, miRNA target prediction, transcription factor target prediction and mechanistic models of gene network regulation. Predicted miRNA functions were either validated experimentally or compared to published data. The predicted miRNA functions are accessible in the miRNA bodymap, an interactive online compendium and mining tool of high-dimensional newly generated and published miRNA expression profiles. The miRNA bodymap enables prioritization of candidate miRNAs based on their expression pattern or functional annotation across tissue or disease subgroup. The miRNA bodymap project provides users with a single one-stop data-mining solution and has great potential to become a community resource

High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA

MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs implicated in a wide variety of cellular processes. Research in this field is accelerating, and the growing number of miRNAs emphasizes the need for high-throughput and sensitive detection methods. Here we present the successful evaluation of the Megaplex reverse transcription format of the stem-loop primer-based real-time quantitative polymerase chain reaction (RT-qPCR) approach to quantify miRNA expression. The Megaplex reaction provides simultaneous reverse transcription of 450 mature miRNAs, ensuring high-throughput detection. Further, the introduction of a complementary DNA pre-amplification step significantly reduces the amount of input RNA needed, even down to single-cell level. To evaluate possible pre-amplification bias, we compared the expression of 384 miRNAs in three different cancer cell lines with Megaplex RT, with or without an additional pre-amplification step. The normalized Cq values of all three sample pairs showed a good correlation with maintenance of differential miRNA expression between the cell lines. Moreover, pre-amplification using 10 ng of input RNA enabled the detection of miRNAs that were undetectable when using Megaplex alone with 400 ng of input RNA. The high specificity of RT-qPCR together with a superior sensitivity makes this approach the method of choice for high-throughput miRNA expression profiling

Real-time quantification of microRNAs by stem–loop RT–PCR

A novel microRNA (miRNA) quantification method has been developed using stem–loop RT followed by TaqMan PCR analysis. Stem–loop RT primers are better than conventional ones in terms of RT efficiency and specificity. TaqMan miRNA assays are specific for mature miRNAs and discriminate among related miRNAs that differ by as little as one nucleotide. Furthermore, they are not affected by genomic DNA contamination. Precise quantification is achieved routinely with as little as 25 pg of total RNA for most miRNAs. In fact, the high sensitivity, specificity and precision of this method allows for direct analysis of a single cell without nucleic acid purification. Like standard TaqMan gene expression assays, TaqMan miRNA assays exhibit a dynamic range of seven orders of magnitude. Quantification of five miRNAs in seven mouse tissues showed variation from less than 10 to more than 30 000 copies per cell. This method enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases. Stem–loop RT–PCR can be used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs). Furthermore, the concept of stem–loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency

South China Sea hydrological changes and Pacific Walker Circulation variations over the last millennium

© Macmillan Publishers Limited, 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 2 (2011): 293, doi:10.1038/ncomms1297.The relative importance of north–south migrations of the intertropical convergence zone (ITCZ) versus El Niño-Southern Oscillation and its associated Pacific Walker Circulation (PWC) variability for past hydrological change in the western tropical Pacific is unclear. Here we show that north–south ITCZ migration was not the only mechanism of tropical Pacific hydrologic variability during the last millennium, and that PWC variability profoundly influenced tropical Pacific hydrology. We present hydrological reconstructions from Cattle Pond, Dongdao Island of the South China Sea, where multi-decadal rainfall and downcore grain size variations are correlated to the Southern Oscillation Index during the instrumental era. Our downcore grain size reconstructions indicate that this site received less precipitation during relatively warm periods, AD 1000–1400 and AD 1850–2000, compared with the cool period (AD 1400–1850). Including our new reconstructions in a synthesis of tropical Pacific records results in a spatial pattern of hydrologic variability that implicates the PWC.This work was supported by the Natural Science Foundation of China (NSFC) (40730107) and the Major State Basic Research Development Program of China (973 Program) (No.2010CB428902). DWO acknowledges support from the US NSF

Automatic home video abstraction using audio contents

With the increasing number of people who can afford to make videos to record their lives, home videos play more and more important role in people’s lives. Video abstraction is an efficient way to help review such a huge amount of home videos. In this paper, an automatic home video abstraction method mainly using audio contents is presented. The audio contents are first segmented and classified as speech, music, silence and special sounds basing on audio short-time features and morphology. Then special sounds are further categorized as songs, laughter, applause, scream and others using Hidden Markov Model (HMM). After that, motion level and blur degree are acquired using the video contents. Finally, video segments containing special effects, such as speech, laughter, song, applause, scream, and specified motion level and blur degree, are extracted as the main parts of the abstract. The remaining parts of the abstract are generated using key frame information. The experimental results show that the proposed algorithm can extract desired parts of home video to generate satisfactory video abstracts