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Gene noise

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https://www.readbyqxmd.com/read/27914298/effects-of-environmental-noise-exposure-on-dna-methylation-in-the-brain-and-metabolic-health
#1
Liqiong Guo, Peng-Hui Li, Hua Li, Elena Colicino, Silvia Colicino, Yi Wen, Ruiping Zhang, Xiaotian Feng, Timothy M Barrow, Akin Cayir, Andrea A Baccarelli, Hyang-Min Byun
Environmental noise exposure is associated with adverse effects on human health including hearing loss, heart disease, and changes in stress-related hormone levels. Alteration in DNA methylation in response to environmental exposures is a well-known phenomenon and it is implicated in many human diseases. Understanding how environmental noise exposures affect DNA methylation patterns may help to elucidate the link between noise and adverse effects on health. In this pilot study we examined the effects of environmental noise exposure on DNA methylation of genes related to brain function and investigated whether these changes are related with metabolic health...
November 30, 2016: Environmental Research
https://www.readbyqxmd.com/read/27911933/driving-cells-to-the-desired-state-in-a-bimodal-distribution-through-manipulation-of-internal-noise-with-biologically-practicable-approaches
#2
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
https://www.readbyqxmd.com/read/27911801/mechanical-bounds-to-transcriptional-noise
#3
Stuart A Sevier, David A Kessler, Herbert Levine
Over the past several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Although many stochastic effects have been explained, the source of transcriptional bursting (one of the most well-known sources of stochasticity) has continued to evade understanding. Recent results have pointed to mechanical feedback as the source of transcriptional bursting, but a reconciliation of this perspective with preexisting views of transcriptional regulation is lacking...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#4
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27905558/microrna-mir-34-provides-robustness-to-environmental-stress-response-via-the-daf-16-network-in-c-elegans
#5
Meltem Isik, T Keith Blackwell, Eugene Berezikov
Diverse stresses and aging alter expression levels of microRNAs, suggesting a role for these posttranscriptional regulators of gene expression in stress modulation and longevity. Earlier studies demonstrated a central role for the miR-34 family in promoting cell cycle arrest and cell death following stress in human cells. However, the biological significance of this response was unclear. Here we show that in C. elegans mir-34 upregulation is necessary for developmental arrest, correct morphogenesis, and adaptation to a lower metabolic state to protect animals against stress-related damage...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902489/effects-of-cell-cycle-noise-on-excitable-gene-circuits
#6
Alan Veliz-Cuba, Chinmaya Gupta, Matthew R Bennett, Krešimir Josić, William Ott
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a three-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks...
November 30, 2016: Physical Biology
https://www.readbyqxmd.com/read/27899659/discovery-and-validation-of-information-theory-based-transcription-factor-and-cofactor-binding-site-motifs
#7
Ruipeng Lu, Eliseos J Mucaki, Peter K Rogan
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899641/3d-genome-structure-modeling-by-lorentzian-objective-function
#8
Tuan Trieu, Jianlin Cheng
The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899618/rna-seq-mixology-designing-realistic-control-experiments-to-compare-protocols-and-analysis-methods
#9
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897008/tracing-co-regulatory-network-dynamics-in-noisy-single-cell-transcriptome-trajectories
#10
Pablo Cordero, Joshua M Stuart
The availability of gene expression data at the single cell level makes it possible to probe the molecular underpinnings of complex biological processes such as differentiation and oncogenesis. Promising new methods have emerged for reconstructing a progression 'trajectory' from static single-cell transcriptome measurements. However, it remains unclear how to adequately model the appreciable level of noise in these data to elucidate gene regulatory network rewiring. Here, we present a framework called Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR) that infers progressions from static single-cell transcriptomes by employing a continuous parametrization of Gaussian mixtures in high-dimensional curves...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896962/adaptive-testing-of-snp-brain-functional-connectivity-association-via-a-modular-network-analysis
#11
Chen Gao, Junghi Kim, Wei Pan
Due to its high dimensionality and high noise levels, analysis of a large brain functional network may not be powerful and easy to interpret; instead, decomposition of a large network into smaller subcomponents called modules may be more promising as suggested by some empirical evidence. For example, alteration of brain modularity is observed in patients suffering from various types of brain malfunctions. Although several methods exist for estimating brain functional networks, such as the sample correlation matrix or graphical lasso for a sparse precision matrix, it is still difficult to extract modules from such network estimates...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27894947/strategies-to-identify-natural-antisense-transcripts
#12
REVIEW
Yulong Sun, Dijie Li, Ru Zhang, Shang Peng, Ge Zhang, Tuanming Yang, Airong Qian
Natural antisense transcripts, originally considered as transcriptional noises arising from so-called "junk DNA", are recently recognized as important modulators for gene regulation. They are prevalent in nearly all realms of life and have been found to modulate gene expression positively or negatively. By affecting almost all stages of gene expression range from pre-transcriptional, transcriptional and post-transcriptional to translation, NATs are fundamentally involved in various biological processes. However, compared to increasing huge data from transcriptional analysis especially high-throughput sequencing technologies (such as RNA-seq), limited functional NATs (around 70) are so far reported, which hinder our advanced comprehensive understanding for this field...
November 25, 2016: Biochimie
https://www.readbyqxmd.com/read/27893768/macromolecular-crowding-regulates-the-gene-expression-profile-by-limiting-diffusion
#13
Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R Petzold
We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27892712/variability-in-metagenomic-count-data-and-its-influence-on-the-identification-of-differentially-abundant-genes
#14
Viktor Jonsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27888167/delta-notch-signalling-in-segmentation
#15
Bo-Kai Liao, Andrew C Oates
Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor...
November 22, 2016: Arthropod Structure & Development
https://www.readbyqxmd.com/read/27883134/non-fluorescent-quantification-of-single-mrna-with-transient-absorption-microscopy
#16
Jing Liu, Joseph M K Irudayaraj
Single molecule detection is confounded by the background signals from the biological environment, such as autofluorescence, Rayleigh scattering, or turbidity in cells and tissues. In this article, we report on the utilization of gold nanoparticles (AuNPs) as an orthogonal probe for non-fluorescence detection of single molecules with a transient absorption microscopy (TAM). The developed system and concepts were validated by quantitative evaluation of human epidermal receptor 2 (Her2) mRNA in cancer cells and tissues at single copy sensitivity...
November 24, 2016: Nanoscale
https://www.readbyqxmd.com/read/27876759/vertical-flow-array-chips-reliably-identify-cell-types-from-single-cell-mrna-sequencing-experiments
#17
Masataka Shirai, Koji Arikawa, Kiyomi Taniguchi, Maiko Tanabe, Tomoyuki Sakai
Single-cell mRNA sequencing offers an unbiased approach to dissecting cell types as functional units in multicellular tissues. However, highly reliable cell typing based on single-cell gene expression analysis remains challenging because of the lack of methods for efficient sample preparation for high-throughput sequencing and evaluating the statistical reliability of the acquired cell types. Here, we present a highly efficient nucleic reaction chip (a vertical flow array chip (VFAC)) that uses porous materials to reduce measurement noise and improve throughput without a substantial increase in reagent...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27875323/estimating-intrinsic-and-extrinsic-noise-from-single-cell-gene-expression-measurements
#18
Audrey Qiuyan Fu, Lior Pachter
Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from two-reporter assays that probe expression of identically regulated gene pairs in single cells. We examine established formulas [Elowitz, M. B., A. J. Levine, E. D. Siggia and P. S. Swain (2002): "Stochastic gene expression in a single cell," Science, 297, 1183-1186.] for the estimation of intrinsic and extrinsic noise and provide interpretations of them in terms of a hierarchical model...
December 1, 2016: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/27872618/time-series-analysis-of-the-bacillus-subtilis-sporulation-network-reveals-low-dimensional-chaotic-dynamics
#19
Paola Lecca, Ivan Mura, Angela Re, Gary C Barker, Adaoha E C Ihekwaba
Chaotic behavior refers to a behavior which, albeit irregular, is generated by an underlying deterministic process. Therefore, a chaotic behavior is potentially controllable. This possibility becomes practically amenable especially when chaos is shown to be low-dimensional, i.e., to be attributable to a small fraction of the total systems components. In this case, indeed, including the major drivers of chaos in a system into the modeling approach allows us to improve predictability of the systems dynamics. Here, we analyzed the numerical simulations of an accurate ordinary differential equation model of the gene network regulating sporulation initiation in Bacillus subtilis to explore whether the non-linearity underlying time series data is due to low-dimensional chaos...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27867061/interaction-between-drd2-variation-and-sound-environment-on-mood-and-emotion-related-brain-activity
#20
T Quarto, M C Fasano, P Taurisano, L Fazio, L A Antonucci, B Gelao, R Romano, M Mancini, A Porcelli, R Masellis, K J Pallesen, A Bertolino, G Blasi, E Brattico
Sounds, like music and noise, are capable of reliably affecting individuals' mood and emotions. However, these effects are highly variable across individuals. A putative source of variability is genetic background. Here we explored the interaction between a functional polymorphism of the dopamine D2 receptor gene (DRD2 rs1076560, G>T, previously associated with the relative expression of D2S/L isoforms) and sound environment on mood and emotion-related brain activity. Thirty-eight healthy subjects were genotyped for DRD2 rs1076560 (G/G=26; G/T=12) and underwent functional magnetic resonance imaging (fMRI) during performance of an implicit emotion-processing task while listening to music or noise...
November 17, 2016: Neuroscience
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