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Transcriptional grammar

R E Motyer, S Liddy, W C Torreggiani, O Buckley
BACKGROUND: Voice recognition (VR) dictation of radiology reports has become the mainstay of reporting in many institutions worldwide. Despite benefit, such software is not without limitations, and transcription errors have been widely reported. AIM: Evaluate the frequency and nature of non-clinical transcription error using VR dictation software. METHODS: Retrospective audit of 378 finalised radiology reports. Errors were counted and categorised by significance, error type and sub-type...
October 1, 2016: Irish Journal of Medical Science
Ashley J Waardenberg, Bernou Homan, Stephanie Mohamed, Richard P Harvey, Romaric Bouveret
The ability to accurately predict the DNA targets and interacting cofactors of transcriptional regulators from genome-wide data can significantly advance our understanding of gene regulatory networks. NKX2-5 is a homeodomain transcription factor that sits high in the cardiac gene regulatory network and is essential for normal heart development. We previously identified genomic targets for NKX2-5 in mouse HL-1 atrial cardiomyocytes using DNA-adenine methyltransferase identification (DamID). Here, we apply machine learning algorithms and propose a knowledge-based feature selection method for predicting NKX2-5 protein : protein interactions based on motif grammar in genome-wide DNA-binding data...
September 2016: Open Biology
Rupinder Sayal, Jacqueline M Dresch, Irina Pushel, Benjamin R Taylor, David N Arnosti
Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency...
2016: ELife
Brian MacWhinney, Davida Fromm
AphasiaBank has used a standardized protocol to collect narrative, procedural, personal, and descriptive discourse from 290 persons with aphasia, as well as 190 control participants. These data have been transcribed in the Codes for the Human Analysis of Transcripts (CHAT) format for analysis by the Computerized Language Analysis (CLAN) programs. Here, we review results from 45 studies based on these data that investigate aphasic productions in terms of these eight areas: discourse, grammar, lexicon, gesture, fluency, syndrome classification, social factors, and treatment effects...
February 2016: Seminars in Speech and Language
Joseph Grice, Boris Noyvert, Laura Doglio, Greg Elgar
BACKGROUND: Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive...
2015: PloS One
Aliccia Bollig-Fischer, Luca Marchetti, Cristina Mitrea, Jiusheng Wu, Adéle Kruger, Vincenzo Manca, Sorin Drăghici
MOTIVATION: Oncogenes are known drivers of cancer phenotypes and targets of molecular therapies; however, the complex and diverse signaling mechanisms regulated by oncogenes and potential routes to targeted therapy resistance remain to be fully understood. To this end, we present an approach to infer regulatory mechanisms downstream of the HER2 driver oncogene in SUM-225 metastatic breast cancer cells from dynamic gene expression patterns using a succession of analytical techniques, including a novel MP grammars method to mathematically model putative regulatory interactions among sets of clustered genes...
November 1, 2014: Bioinformatics
Lucy Hiscox, Erika Leonavičiūtė, Trevor Humby
Dyslexia is associated with difficulties in language-specific skills such as spelling, writing and reading; the difficulty in acquiring literacy skills is not a result of low intelligence or the absence of learning opportunity, but these issues will persist throughout life and could affect long-term education. Writing is a complex process involving many different functions, integrated by the working memory system; people with dyslexia have a working memory deficit, which means that concentration on writing quality may be detrimental to understanding...
August 2014: Dyslexia: the Journal of the British Dyslexia Association
Oliver Purcell, Jean Peccoud, Timothy K Lu
To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger functional units. Here, we develop a grammar for the design of synthetic transcription factors (sTFs) in eukaryotic cells and implement it within GenoCAD, a Computer-Aided Design (CAD) software for synthetic biology...
October 17, 2014: ACS Synthetic Biology
Vanja Haberle, Nan Li, Yavor Hadzhiev, Charles Plessy, Christopher Previti, Chirag Nepal, Jochen Gehrig, Xianjun Dong, Altuna Akalin, Ana Maria Suzuki, Wilfred F J van IJcken, Olivier Armant, Marco Ferg, Uwe Strähle, Piero Carninci, Ferenc Müller, Boris Lenhard
A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs and recruits general transcription factors to initiate transcription. The nature and causative relationship of the DNA sequence and chromatin signals that govern the selection of most TSSs by RNA polymerase II remain unresolved. Maternal to zygotic transition represents the most marked change of the transcriptome repertoire in the vertebrate life cycle. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the tenth cell cycle, marking the mid-blastula transition...
March 20, 2014: Nature
Shira Weingarten-Gabbay, Eran Segal
Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the set of rules that govern basic principles in transcriptional regulation, the functional elements involved, and the ways in which they combine to orchestrate a transcriptional output. Here, we review the current understanding of various grammatical rules, including the effect on expression of the number of transcription factor binding sites, their location, orientation, affinity and activity; co-association with different factors; and intrinsic nucleosome organization...
June 2014: Human Genetics
Marcelo Rubinstein, Flávio S J de Souza
Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time...
December 19, 2013: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Esteban O Mazzoni, Shaun Mahony, Michael Closser, Carolyn A Morrison, Stephane Nedelec, Damian J Williams, Disi An, David K Gifford, Hynek Wichterle
Efficient transcriptional programming promises to open new frontiers in regenerative medicine. However, mechanisms by which programming factors transform cell fate are unknown, preventing more rational selection of factors to generate desirable cell types. Three transcription factors, Ngn2, Isl1 and Lhx3, were sufficient to program rapidly and efficiently spinal motor neuron identity when expressed in differentiating mouse embryonic stem cells. Replacement of Lhx3 by Phox2a led to specification of cranial, rather than spinal, motor neurons...
September 2013: Nature Neuroscience
Frøydis Morken, Turid Helland
Research on dyslexia has largely centred on reading. The aim of this study was to assess the writing of 13 children with and 28 without dyslexia at age 11 years. A programme for keystroke logging was used to allow recording of typing activity as the children performed a sentence dictation task. Five sentences were read aloud twice each. The task was to type the sentence as correctly as possible, with no time constraints. The data were analysed from a product (spelling, grammar and semantics) and process (transcription fluency and revisions) perspective, using repeated measures ANOVA and t-tests to investigate group differences...
August 2013: Dyslexia: the Journal of the British Dyslexia Association
Sutapa Datta, Subhasis Mukhopadhyay
An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions...
2013: PloS One
Andrew Paul Hutchins, Siew Hua Choo, Tapan Kumar Mistri, Mehran Rahmani, Chow Thai Woon, Calista Keow Leng Ng, Ralf Jauch, Paul Robson
Transcription factors (TF) often bind in heterodimeric complexes with each TF recognizing a specific neighboring cis element in the regulatory region of the genome. Comprehension of this DNA motif grammar is opaque, yet recent developments have allowed the interrogation of genome-wide TF binding sites. We reasoned that within this data novel motif grammars could be identified that controlled distinct biological programs. For this purpose, we developed a novel motif-discovery tool termed fexcom that systematically interrogates ChIP-seq data to discover spatially constrained TF-TF composite motifs occurring over short DNA distances...
February 2013: Stem Cells
Roee Amit
One of the greatest challenges facing synthetic biology is to develop a technology that allows gene regulatory circuits in microbes to integrate multiple inputs or stimuli using a small DNA sequence "foot-print", and which will generate precise and reproducible outcomes. Achieving this goal is hindered by the routine utilization of the commonplace σ(70) promoters in gene-regulatory circuits. These promoters typically are not capable of integrating binding of more than two or three transcription factors in natural examples, which has limited the field to developing integrated circuits made of two-input biological "logic" gates...
2012: Sub-cellular Biochemistry
Danielle M McCarthy, Katrina A Leone, David H Salzman, John A Vozenilek, Kenzie A Cameron
BACKGROUND: The field of health literacy has closely examined the readability of written health materials to optimize patient comprehension. Few studies have examined spoken communication in a way that is comparable to analyses of written communication. PURPOSE: The study objective was to characterize the structural elements of residents' spoken words while obtaining informed consent. METHODS: Twenty-six resident physicians participated in a simulated informed consent discussion with a standardized patient...
2012: Teaching and Learning in Medicine
Hani Goodarzi, Hamed S Najafabadi, Panos Oikonomou, Todd M Greco, Lisa Fish, Reza Salavati, Ileana M Cristea, Saeed Tavazoie
Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. Despite recent efforts, the vast landscape of RNA regulatory elements remains largely uncharacterized. A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including--but not limited to--transcript stability, alternative splicing and localization...
May 10, 2012: Nature
Anna A Nikulova, Alexander V Favorov, Roman A Sutormin, Vsevolod J Makeev, Andrey A Mironov
Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices...
July 2012: Nucleic Acids Research
Jose S Canovas
It is generally acknowledged that the medium influences the way we communicate and negotiation research directs considerable attention to the impact of different electronic communication modes on the negotiation process and outcomes. Complexity theories offer models and methods that allow the investigation of how pattern and temporal sequences unfold over time in negotiation interactions. By focusing on the dynamic and interactive quality of negotiations as well as the information, choice, and uncertainty contained in the negotiation process, the complexity perspective addresses several issues of central interest in classical negotiation research...
October 2011: Nonlinear Dynamics, Psychology, and Life Sciences
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