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https://www.readbyqxmd.com/read/28544159/simultaneous-measurement-of-t1-b1-and-pharmacokinetic-model-parameters-using-active-contrast-encoding-ace-mri
#1
Jin Zhang, Kerryanne Winters, Olivier Reynaud, Sungheon Gene Kim
The aim of this study was to assess the feasibility of combining dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI) with the measurement of the radiofrequency (RF) transmit field B1 and pre-contrast longitudinal relaxation time T10 . A novel approach has been proposed to simultaneously estimate B1 and T10 from a modified DCE-MRI scan that actively encodes the washout phase of the curve with different amounts of T1 and B1 weighting using multiple flip angles and repetition times, hence referred to as active contrast encoding (ACE)-MRI...
May 22, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28541282/tailing-and-degradation-of-argonaute-bound-small-rnas-protect-the-genome-from-uncontrolled-rnai
#2
Paola Pisacane, Mario Halic
RNAi is a conserved mechanism in which small RNAs induce silencing of complementary targets. How Argonaute-bound small RNAs are targeted for degradation is not well understood. We show that the adenyl-transferase Cid14, a member of the TRAMP complex, and the uridyl-transferase Cid16 add non-templated nucleotides to Argonaute-bound small RNAs in fission yeast. The tailing of Argonaute-bound small RNAs recruits the 3'-5' exonuclease Rrp6 to degrade small RNAs. Failure in degradation of Argonaute-bound small RNAs results in accumulation of 'noise' small RNAs on Argonaute and targeting of diverse euchromatic genes by RNAi...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#3
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28524201/a-computational-framework-for-distinguishing-direct-versus-indirect-interactions-in-human-functional-protein-protein-interaction-networks
#4
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28521011/translation-initiation-events-on-structured-eukaryotic-mrnas-generate-gene-expression-noise
#5
Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy Ramachandran, Pedro Mendes, John Eg McCarthy
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem-loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28505727/multiple-binding-sites-for-transcriptional-repressors-can-produce-regular-bursting-and-enhance-noise-suppression
#6
Iván M Lengyel, Luis G Morelli
Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production. Theoretical studies have assumed a single binding site for the repressor, while in most species it is found that multiple binding sites are arranged in clusters. We study a stochastic description of negative autoregulation with multiple binding sites for the repressor. We find that increasing the number of binding sites induces regular bursting of gene products...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28504701/paused-rna-polymerase-ii-inhibits-new-transcriptional-initiation
#7
Wanqing Shao, Julia Zeitlinger
RNA polymerase II (Pol II) pauses downstream of the transcription initiation site before beginning productive elongation. This pause is a key component of metazoan gene expression regulation. Some promoters have a strong disposition for Pol II pausing and often mediate faster, more synchronous changes in expression. This requires multiple rounds of transcription and thus cannot rely solely on pause release. However, it is unclear how pausing affects the initiation of new transcripts during consecutive rounds of transcription...
May 15, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28499413/ranking-metrics-in-gene-set-enrichment-analysis-do-they-matter
#8
Joanna Zyla, Michal Marczyk, January Weiner, Joanna Polanska
BACKGROUND: There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. METHODS AND RESULTS: In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28489418/studies-on-the-clustering-algorithm-for-analyzing-gene-expression-data-with-a-bidirectional-penalty
#9
Hu Yang, Xiaoqin Liu
This article reports a new clustering method based on the k-means algorithm to high-dimensional gene expression data. The proposed approach makes use of bidirectional penalties to constrain the number of clusters and centroids of clusters to simultaneously determine the unknown number of clusters and handle large amounts of noise in gene expression data. Numeric studies indicate that this algorithm not only performs better in clustering but is also comparable to other approaches in its ability to obtain the correct number of clusters and correct signal features...
May 10, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28483564/the-influence-of-nuclear-compartmentalisation-on-stochastic-dynamics-of-self-repressing-gene-expression
#10
Marc Sturrock, Shiyu Li, Vahid Shahrezaei
Gene expression is an inherently noisy process. This noise is generally thought to be deleterious as precise internal regulation of biochemical reactions is essential for cell growth and survival. Self-repression of gene expression, which is the simplest form of a negative feedback loop, is commonly believed to be employed by cellular systems to decrease the stochastic fluctuations in gene expression. When there is some delay in autoregulation, it is also believed that this system can generate oscillations...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28474674/tradict-enables-accurate-prediction-of-eukaryotic-transcriptional-states-from-100-marker-genes
#11
Surojit Biswas, Konstantin Kerner, Paulo José Pereira Lima Teixeira, Jeffery L Dangl, Vladimir Jojic, Philip A Wigge
Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell...
May 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28470011/joint-l1-2-norm-constraint-and-graph-laplacian-pca-method-for-feature-extraction
#12
Chun-Mei Feng, Ying-Lian Gao, Jin-Xing Liu, Juan Wang, Dong-Qin Wang, Chang-Gang Wen
Principal Component Analysis (PCA) as a tool for dimensionality reduction is widely used in many areas. In the area of bioinformatics, each involved variable corresponds to a specific gene. In order to improve the robustness of PCA-based method, this paper proposes a novel graph-Laplacian PCA algorithm by adopting L1/2 constraint (L1/2 gLPCA) on error function for feature (gene) extraction. The error function based on L1/2-norm helps to reduce the influence of outliers and noise. Augmented Lagrange Multipliers (ALM) method is applied to solve the subproblem...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28466003/gene-feature-extraction-based-on-nonnegative-dual-graph-regularized-latent-low-rank-representation
#13
Guoliang Yang, Zhengwei Hu
Aiming at the problem of gene expression profile's high redundancy and heavy noise, a new feature extraction model based on nonnegative dual graph regularized latent low-rank representation (NNDGLLRR) is presented on the basis of latent low-rank representation (Lat-LRR). By introducing dual graph manifold regularized constraint, the NNDGLLRR can keep the internal spatial structure of the original data effectively and improve the final clustering accuracy while segmenting the subspace. The introduction of nonnegative constraints makes the computation with some sparsity, which enhances the robustness of the algorithm...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28458660/activity-abundance-and-localization-of-quorum-sensing-receptors-in-vibrio-harveyi
#14
Nicola Lorenz, Jae Yen Shin, Kirsten Jung
Quorum sensing (QS) is a process enabling a bacterial population to communicate via small molecules called autoinducers (AIs). This intercellular communication process allows single cells to synchronize their behavior within a population. The marine bacterium Vibrio harveyi ATCC BAA-1116 channels the information of three AI signals into one QS cascade. Three receptors perceive these AIs, the hybrid histidine kinases LuxN, Lux(P)Q and CqsS, to transduce the information to the histidine phosphotransfer (HPt) protein LuxU via phosphorelay, and finally to the response regulator LuxO...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#15
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28438642/diagnostic-microarray-for-14-water-and-foodborne-pathogens-using-a-flatbed-scanner
#16
Vidya Srinivasan, Robert D Stedtfeld, Dieter M Tourlousse, Samuel W Baushke, Yu Xin, Sarah M Miller, Trinh Pham, Jean-Marie Rouillard, Erdogan Gulari, James M Tiedje, Syed A Hashsham
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology...
April 23, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28437444/transcriptional-bursting-in-drosophila-development-stochastic-dynamics-of-eve-stripe-2-expression
#17
David M Holloway, Alexander V Spirov
Anterior-posterior (AP) body segmentation of the fruit fly (Drosophila) is first seen in the 7-stripe spatial expression patterns of the pair-rule genes, which regulate downstream genes determining specific segment identities. Regulation of pair-rule expression has been extensively studied for the even-skipped (eve) gene. Recent live imaging, of a reporter for the 2nd eve stripe, has demonstrated the stochastic nature of this process, with 'bursts' in the number of RNA transcripts being made over time. We developed a stochastic model of the spatial and temporal expression of eve stripe 2 (binding by transcriptional activators (Bicoid and Hunchback proteins) and repressors (Giant and Krüppel proteins), transcriptional initiation and termination; with all rate parameters constrained by features of the experimental data) in order to analyze the noisy experimental time series and test hypotheses for how eve transcription is regulated...
2017: PloS One
https://www.readbyqxmd.com/read/28432993/chemical-biological-and-dna-markers-for-tracing-slaughterhouse-effluent
#18
P J Harvey, M P Taylor, H K Handley, S Foster, M R Gillings, A J Asher
Agricultural practices, if not managed correctly, can have a negative impact on receiving environments via waste disposal and discharge. In this study, a chicken slaughter facility on the rural outskirts of Sydney, Australia, has been identified as a possible source of persistent effluent discharge into a peri-urban catchment. Questions surrounding the facility's environmental management practices go back more than four decades. Despite there having never been a definitive determination of the facility's impact on local stream water quality, the New South Wales Environment Protection Authority (NSW EPA) has implemented numerous pollution reduction requirements to manage noise and water pollution at the slaughter facility...
April 26, 2017: Environmental Research
https://www.readbyqxmd.com/read/28427910/stochasticity-of-gene-expression-as-a-motor-of-epigenetics-in-bacteria-from-individual-to-collective-behavior
#19
REVIEW
Stéphanie Bury-Moné, Bianca Sclavi
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Stochastic gene expression can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by specific genetic network architecture...
April 18, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28427183/withdrawn-random-walk-based-method-to-identify-prognostic-genes-in-colorectal-cancer
#20
Xue Yang, Chen Zhao, Ning An
Ahead of Print article withdrawn by publisher.
March 2, 2017: Oncotarget
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