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Afonina Zhanna A ZA Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, - - 2014
The polyribosomes newly formed on recombinant GFP-encoding mRNAs in a wheat germ cell-free translation system were analyzed using cryo-electron tomography, with sub-tomogram averaging of polysomal ribosomes and reconstruction of 3D structures of individual polyribosomes. The achieved level of resolution in the reconstructed polyribosomes allowed deducing the mRNA path by connecting ...
Bai Na N From the *State Key Laboratory of Oral Disease, Sichuan University, Chengdu, Sichuan; †Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan; ‡Department of Oral and Maxillofacial & Head and Neck Surgery, Medical College and Affiliated Hospital, Qingdao University, Qingdao; and §Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Tianjin Medical University, Tianjin, People's Republic of - - 2014
Because cleft palate (CP) is one of the most common congenital deformities, surgeons have tried for longtime to achieve an ideal reconstruction of the palatal bone defects and restoration of muscle attachments. In this study, a new CP model on rhesus was established and corrected by an approach of distraction ...
Gallego Romero Irene - - 2014
The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be corrected via data normalization, or whether different transcripts are degraded at different rates, potentially ...
Kaplan David D Pathfinder Biotech, Cleveland, OH; Department of Pathology, University Hospitals Case Medical Center and Case Western Reserve University, Cleveland, - - 2014
The E2997 Phase III trial included preservation of valuable chronic lymphocytic leukemia (CLL) patient specimens and relevant clinical outcome data. Using a novel high-resolution technology on a flow cytometry platform, we assessed 79 E2997 samples for the expression of 27 analytes that reflected the activity of signaling pathways and apoptosis. ...
Buckley Martin S MS Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Electronic address: - - 2014
Over the past twenty years, exciting developments in optical and molecular imaging approaches have allowed researchers to examine with unprecedented resolution the spatial organization of transcription sites in the nucleus. An attractive model that has developed from these studies is that active genes cluster to preformed transcription factories that contain ...
Müller Adrienne A Center for Radiopharmaceutical Sciences, ETH Zurich, Zurich, Switzerland. Electronic address: - - 2014
Atherosclerotic plaque rupture is the primary cause for myocardial infarction and stroke. During plaque progression macrophages and mast cells secrete matrix-degrading proteolytic enzymes, such as matrix metalloproteinases (MMPs). We studied levels of MMPs and tissue inhibitor of metalloproteinases-3 (TIMP-3) in relation to the characteristics of carotid plaques. We evaluated in ...
Harris Richard J RJ Department of Psychology and York Neuroimaging Centre, University of York, York YO10 5DD United - - 2014
Although different brain regions are widely considered to be involved in the recognition of facial identity and expression, it remains unclear how these regions process different properties of the visual image. Here, we ask how surface-based reflectance information and edge-based shape cues contribute to the perception and neural representation of ...
Jangi Mohini M David H. Koch Institute for Integrative Cancer - - 2014
The tight regulation of splicing networks is critical for organismal development. To maintain robust splicing patterns, many splicing factors autoregulate their expression through alternative splicing-coupled nonsense-mediated decay (AS-NMD). However, as negative autoregulation results in a self-limiting window of splicing factor expression, it is unknown how variations in steady-state protein levels ...
Tay Yvonne Y Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, - - 2014
In a recent issue of Nature, Kumar et al. demonstrate that the oncogenic potential of the Hmga2 gene is largely due to the ability of its transcript to operate as a competing endogenous RNA in a protein coding-independent manner. The Hmga2 mRNA decoys the let-7 microRNA family to regulate Tgfbr3 ...
Spedito Alessandro A Dipartimento di Biologia e Biotecnologie, Laboratorio di Biologia Cellulare e Neurobiologia, Università degli Studi di Pavia, Via Ferrata 1, Pavia, - - 2014
A new method is proposed which combines the high spatial resolution of transmission electron microscopy with information on the dynamics of transcription. Incorporation of two different RNA precursors was used to define a time transcription window on cultured cells treated with hypometabolizing peptides which are known to modulate transcription. This ...
Yan Wen-Jing WJ State Key Laboratory of Brain and Cognitive Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, China ; University of Chinese Academy of Sciences, Beijing, - - 2014
A robust automatic micro-expression recognition system would have broad applications in national safety, police interrogation, and clinical diagnosis. Developing such a system requires high quality databases with sufficient training samples which are currently not available. We reviewed the previously developed micro-expression databases and built an improved one (CASME II), with ...
Seo Joonbae J Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, - - 2014
The dynamic process of pre-mRNA splicing is regulated by combinatorial control exerted by overlapping cis-elements that are unique to every exon and its flanking intronic sequences. Splicing cis-elements are usually 4-8-nucleotide-long linear motifs that furnish interaction sites for specific proteins. Secondary and higher-order RNA structures exert an additional layer of ...
Plass Mireya M Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, - - 2014
In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or hindering the interaction ...
Patil Deepak P DP Center for RNA Biology, The Ohio State University, Columbus, OH, - - 2014
mRNA polyadenylation functions in nuclear export, translation, and stability. We describe an efficient protocol designed to assess poly(A) tail length that is based on 3' tailing by yeast poly(A) polymerase and product analysis to single-nucleotide resolution by capillary electrophoresis.
Speth Corinna C Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, - - 2014
Quantitative real-time PCR (qRT-PCR) is a common technique for mRNA quantification. Several methods have been developed in the past few years in order to adapt qRT-PCR also for small non-coding RNAs (sRNA). We here provide a simple and sensitive protocol that allows quantification of mRNAs, selected sRNAs, and long non-coding ...
Schlederer Michaela M Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, - - 2014
In targeted therapy, patient tumors are analyzed for aberrant activations of core cancer pathways, monitored based on biomarker expression, to ensure efficient treatment. Thus, diagnosis and therapeutic decisions are often based on the status of biomarkers determined by immunohistochemistry in combination with other clinical parameters. Standard evaluation of cancer specimen ...
Machida Ryuji J RJ Biodiversity Research Centre, Academia Sinica, Nankang, Taipei, - - 2014
The 5' untranslated regions of mRNA play an important role in their translation. Here, we describe the development of four methods of profiling mRNA 5' ends using the Illumina sequencing platform; the first method utilizes SMART (Switching Mechanism At 5' end of RNA Transcript) technology, while the second involves replacing ...
Skene Peter J PJ Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United - - 2014
RNA polymerase II (PolII) transcribes RNA within a chromatin context, with nucleosomes acting as barriers to transcription. Despite these barriers, transcription through chromatin in vivo is highly efficient, suggesting the existence of factors that overcome this obstacle. To increase the resolution obtained by standard chromatin immunoprecipitation, we developed a novel ...
Li Xiangqi X Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, - - 2013
Since the first miRNA was discovered in 1993, miRNAs have become a hotspot for biological research. In order to feed this demand, a robust method is required to detect miRNA gene expression. Development of a detection method is more difficult for miRNAs than for long RNAs, such as mRNA, owing ...
Baas Roy R 1Department of Molecular Cancer Research, University Medical Centre, Utrecht, The - - 2013
Posttranslational modifications of histones play an important role in the regulation of gene expression and chromatin structure in eukaryotes. The balance between chromatin factors depositing (writers) and removing (erasers) histone marks regulates the steady-state levels of chromatin modifications. Here we describe a novel microscopy-based screening method to identify proteins that ...
Schwartz Schraga S Broad Institute of MIT and Harvard, Cambridge, MA 02142, - - 2013
N(6)-methyladenosine (m(6)A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m(6)A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of ...
Tebaldi T - - 2013
High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different '-omics'. It has been recently demonstrated that translational control is a widespread phenomenon, ...
Steijger Tamara T European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, - - 2013
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even ...
Safikhani Zhaleh - - 2013
Recent advances in the sequencing technologies have provided a handful of RNA-seq datasets for transcriptome analysis. However, reconstruction of full-length isoforms and estimation of the expression level of transcripts with a low cost is a challenging task. We propose a novel de novo method named SSP that incorporate Interval Integer ...
Liu Nian - - 2013
N(6)-methyladenosine (m(6)A) is the most abundant modification in mammalian mRNA and long noncoding RNA (lncRNA). Recent discoveries of two m(6)A demethylases and cell-type and cell-state-dependent m(6)A patterns indicate that m(6)A modifications are highly dynamic and likely play important biological roles for RNA akin to DNA methylation or histone modification. Proposed ...
Khan Zia Z Department of Human Genetics, University of Chicago, Chicago, IL 60637, - - 2013
Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which ...
Behr Jonas - - 2013
High throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape pose profound computational challenges for transcriptome ...
Phan Trang Thi Phuong - - 2013
Different mRNA stabilizing elements including the 3'-stem-loop, the ribosome binding sites (RBS), the 5'-stem-loop and the spacer region between the RBS and the 5'-stem-loop were analysed in detail to increase mRNA stability resulting in enhanced expression of heterologous proteins. In addition, in combination with mRNA stabilizing elements, we propose a ...
Toffano-Nioche Claire - - 2013
The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few ...
Peng Yu - - 2013
RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which make it ...
Castelnuovo Manuele - - 2013
Many Saccharomyces cerevisiae genes encode antisense transcripts, some of which are unstable and degraded by the exosome component Rrp6. Loss of Rrp6 results in the accumulation of long PHO84 antisense (AS) RNAs and repression of sense transcription through PHO84 promoter deacetylation. We used single-molecule resolution fluorescent in situ hybridization (smFISH) ...
Lee Kyoung-Uk - - 2013
In recent years there has been an enormous increase of neuroscience research using the facial expressions of emotion. This has led to a need for ethnically specific facial expressions data, due to differences of facial emotion processing among different ethnicities. FIFTY PROFESSIONAL ACTORS WERE ASKED TO POSE WITH EACH OF ...
Eliscovich Carolina C Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, - - 2013
Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown ...
Hennig Bianca P - - 2013
The eukaryotic chromatin structure is essential in correctly defining transcription units. Impairing this structure can activate cryptic promoters, and lead to the accumulation of aberrant RNA transcripts. Here we discuss critical pathways that are responsible for the repression of cryptic transcription and the maintenance of genome integrity.
Mutalik Vivek K - - 2013
An inability to reliably predict quantitative behaviors for novel combinations of genetic elements limits the rational engineering of biological systems. We developed an expression cassette architecture for genetic elements controlling transcription and translation initiation in Escherichia coli: transcription elements encode a common mRNA start, and translation elements use an overlapping ...
Lin-Moshier Yaping Y Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, - - 2013
Often experimentalists require a quantitative assessment of the levels of heterologously expressed proteins to best interpret changed Ca(2+) signaling patterns. Here, we detail a rapid and convenient western blotting method for individual Xenopus oocytes. The method exploits recently introduced rapid blotting systems, commercially available from Invitrogen (iBlot) or Bio-Rad (Trans-Blot ...
Inada Toshifumi - - 2013
RNA processing is an essential gene expression step and plays a crucial role to achieve diversity of gene products in eukaryotes. Various aberrant mRNAs transiently produced during RNA processing reactions are recognized and eliminated by specific quality control systems. It has been demonstrated that these mRNA quality control systems stimulate ...
Qing Tao - - 2013
RNA-Seq promises to be used in clinical settings as a gene-expression profiling tool; however, questions about its variability and biases remain and need to be addressed. Thus, RNA controls with known concentrations and sequence identities originally developed by the External RNA Control Consortium (ERCC) for microarray and qPCR platforms have ...
Park Juw Won - - 2013
RNA sequencing (RNA-Seq) has emerged as a powerful and increasingly cost-effective technology for analysis of transcriptomes. RNA-Seq has several significant advantages over gene expression microarrays, including its high sensitivity and accuracy, broad dynamic range, nucleotide-level resolution, ability to detect novel mRNA transcripts, and ability to analyze pre-mRNA alternative splicing. A ...
Kawai Nobuyuki - - 2013
A Noh mask, worn by expert actors during performance on the Japanese traditional Noh drama, conveys various emotional expressions despite its fixed physical properties. How does the mask change its expressions? Shadows change subtly during the actual Noh drama, which plays a key role in creating elusive artistic enchantment. We ...
Sinha Swati - - 2013
Aebp1 is a transcription factor that negatively regulates adipogenesis and also is upregulated in primary GBM as against secondary GBM. Here we describe a systematic approach to map the in vivo occupancy sites of Aebp1 by using a combination of chromatin immune-precipitation technique and hybridization to Agilent high resolution human ...
Spracklen Andrew J - - 2013
Drosophila oogenesis or follicle development has been widely used to advance the understanding of complex developmental and cell biologic processes. This methods paper describes how to isolate mid-to-late stage follicles (Stage 10B-14) and utilize them to provide new insights into the molecular and morphologic events occurring during tight windows of ...
Mino Takashi T a Laboratory of Infection and Prevention, Department of Biological Responses , Institute for Virus Research, Kyoto University , Kyoto , - - 2013
Cytokines are critical mediators of inflammation and host defense. Cytokine production is regulated during transcription and post-transcription. Post-transcriptional regulation modifies mRNA stability and translation, allowing for the rapid and flexible control of gene expression, which is important for coordinating the initiation and resolution of inflammation. We review here a variety ...
Smith Ezra - - 2012
Emotional faces are motivationally salient stimuli that automatically capture attention and rapidly potentiate neural processing. Because of their superior temporal resolution, scalp-recorded event-related potentials (ERPs) are ideal for examining rapid changes in neural activity. Some reports have found larger ERPs for fearful and angry faces compared to both neutral and ...
Trapnell Cole C Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, - - 2013
Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially ...
Rajaei Mehrdad - - 2012
Polymorphism of variable number of tandem repeats (VNTR) in the promoter region of X-ray repair cross-complementing 5 (MIM: 194364, XRCC5; rs6147172) was reported. The aim of the present study is to evaluate the influence of this polymorphism on XRCC5 mRNA levels. Genotypes of XRCC5 VNTR were determined by high resolution ...
Harris Richard J - - 2012
Whether the brain represents facial expressions as perceptual continua or as emotion categories remains controversial. Here, we measured the neural response to morphed images to directly address how facial expressions of emotion are represented in the brain. We found that face-selective regions in the posterior superior temporal sulcus and the ...
Yoon Hyun Kyung - - 2012
Objective. Aberrant splicing is one of the most significant components generating functional diversity in many pathological conditions. The objective of this study was to analyse the mutations or aberrant splicing of A20 transcript, the region encompassing the ovarian tumour (OTU) domain [which is functionally important as an inhibitor of nuclear ...
Connelly Colleen M CM Department of Chemistry, North Carolina State University, Raleigh, NC 27695, - - 2012
MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene regulators and have been shown to regulate many biological processes including embryonal development, cell differentiation, apoptosis, and proliferation. Variations in the expression of certain miRNAs have been linked to a wide range of human diseases - especially cancer - ...
Darmon Sarah K - - 2012
Polyadenylation is a 3' mRNA processing event that contributes to gene expression by affecting stability, export and translation of mRNA. Human polyadenylation signals (PAS) have core and auxiliary elements that bind polyadenylation factors upstream and downstream of the cleavage site. The majority of mRNAs do not have optimal upstream and ...
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