keyword
MENU ▼
Read by QxMD icon Read
search

Gene noise

keyword
https://www.readbyqxmd.com/read/29778803/age-affects-reinforcement-learning-through-dopamine-based-learning-imbalance-and-high-decision-noise-not-through-parkinsonian-mechanisms
#1
Ravi B Sojitra, Itamar Lerner, Jessica R Petok, Mark A Gluck
Probabilistic reinforcement learning declines in healthy cognitive aging. While some findings suggest impairments are especially conspicuous in learning from rewards, resembling deficits in Parkinson's disease, others also show impairments in learning from punishments. To reconcile these findings, we tested 252 adults from 3 age groups on a probabilistic reinforcement learning task, analyzed trial-by-trial performance with a Q-reinforcement learning model, and correlated both fitted model parameters and behavior to polymorphisms in dopamine-related genes...
April 19, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29776125/post-transcriptional-bursting-in-genes-regulated-by-small-rna-molecules
#2
Guillermo Rodrigo
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29771290/single-cell-clustering-based-on-cell-pair-differentiability-correlation-and-variance-analysis
#3
Hao Jiang, Lydia Sohn, Haiyan Huang, Luonan Chen
Motivation: The rapid advancement of single cell technologies has shed new light on the complex mechanisms of cellular heterogeneity. Identification of intercellular transcriptomic heterogeneity is one of the most critical tasks in single-cell RNA-sequencing studies. Results: We propose a new cell similarity measure based on cell-pair differentiability correlation, which is derived from gene differential pattern among all cell pairs. Through plugging into the framework of hierarchical clustering with this new measure, we further develop a variance analysis based clustering algorithm 'Corr' that can determine cluster number automatically and identify cell types accurately...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29768214/noise-in-the-vertebrate-segmentation-clock-is-boosted-by-time-delays-but-tamed-by-notch-signaling
#4
Sevdenur Keskin, Gnanapackiam S Devakanmalai, Soo Bin Kwon, Ha T Vu, Qiyuan Hong, Yin Yeng Lee, Mohammad Soltani, Abhyudai Singh, Ahmet Ay, Ertuğrul M Özbudak
Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#5
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29754821/a-post-transcriptional-feedback-mechanism-for-noise-suppression-and-fate-stabilization
#6
Maike M K Hansen, Winnie Y Wen, Elena Ingerman, Brandon S Razooky, Cassandra E Thompson, Roy D Dar, Charles W Chin, Michael L Simpson, Leor S Weinberger
Diverse biological systems utilize fluctuations ("noise") in gene expression to drive lineage-commitment decisions. However, once a commitment is made, noise becomes detrimental to reliable function, and the mechanisms enabling post-commitment noise suppression are unclear. Here, we find that architectural constraints on noise suppression are overcome to stabilize fate commitment. Using single-molecule and time-lapse imaging, we find that-after a noise-driven event-human immunodeficiency virus (HIV) strongly attenuates expression noise through a non-transcriptional negative-feedback circuit...
May 4, 2018: Cell
https://www.readbyqxmd.com/read/29746905/chronic-lead-exposure-induces-cochlear-oxidative-stress-and-potentiates-noise-induced-hearing-loss
#7
Samson Jamesdaniel, Rita Rosati, Judy Westrick, Douglas M Ruden
Acquired hearing loss is caused by complex interactions of multiple environmental risk factors, such as elevated levels of lead and noise, which are prevalent in urban communities. This study delineates the mechanism underlying lead-induced auditory dysfunction and its potential interaction with noise exposure. Young-adult C57BL/6 mice were exposed to: 1) control conditions; 2) 2 mM lead acetate in drinking water for 28 days; 3) 90 dB broadband noise 2 h/day for two weeks; and 4) both lead and noise...
May 7, 2018: Toxicology Letters
https://www.readbyqxmd.com/read/29745866/astral-iii-polynomial-time-species-tree-reconstruction-from-partially-resolved-gene-trees
#8
Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
BACKGROUND: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. RESULTS: We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k)...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29738822/the-drosophila-light-activated-trp-and-trpl-channels-targets-of-the-phosphoinositide-signaling-cascade
#9
REVIEW
Ben Katz, Baruch Minke
The Drosophila light-activated Transient Receptor Potential (TRP) channel is the founding member of a large and diverse family of channel proteins. It is now established that TRP channels are evolutionarily conserved and are found in many organisms and tissues. This review outlines the progress made in our understanding of Drosophila phototransduction with a focus on the light sensitive TRP channels. The visual system of Drosophila has remarkable capabilities, such as single photon sensitivity, low dark noise, wide dynamic range of responses to changing ambient light intensities and an unusually wide range of frequency responses to modulated lights...
May 5, 2018: Progress in Retinal and Eye Research
https://www.readbyqxmd.com/read/29733627/engineering-a-functional-small-rna-negative-autoregulation-network-with-model-guided-design
#10
Chelsea Yongxi Hu, Melissa K Takahashi, Yan Zhang, Julius B Lucks
RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal noise. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs...
May 7, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29727603/feature-preserving-noise-reduction-by-using-time-domain-gaussian-weighted-multiple-noise-reduction-filters-for-real-time-bioluminescence-measurement
#11
Keisuke Ishigami, Hiromitsu Furukawa
This paper proposes a time-domain Gaussian-weighted noise reduction filter for bioluminescence measurement with low signal-to-noise ratio through photon counting. The filter was used for estimating the true fold-change signal from noisy gene expression data obtained through real-time dual-color luciferase assay. Furthermore, not only was the higher harmonics noise of the measurement system confirmed to reduce from the gene expression data but rapid and slow changes were also preserved in the estimated signal...
May 1, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29724792/bigscale-an-analytical-framework-for-big-scale-single-cell-data
#12
Giovanni Iacono, Elisabetta Mereu, Amy Guillaumet-Adkins, Roser Corominas, Ivon Cuscó, Gustavo Rodríguez-Esteban, Marta Gut, Luis Alberto Pérez-Jurado, Ivo Gut, Holger Heyn
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers of cells, however, generates extremely large data sets, extending processing time and challenging computing resources. Current scRNA-seq analysis tools are not designed to interrogate large data sets and often lack sensitivity to identify marker genes. With bigSCale, we provide a scalable analytical framework to analyze millions of cells, which addresses the challenges associated with large data sets...
May 3, 2018: Genome Research
https://www.readbyqxmd.com/read/29723572/iteratively-improving-hi-c-experiments-one-step-at-a-time
#13
Rosela Golloshi, Jacob Sanders, Rachel Patton McCord
The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases...
April 30, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29718338/bcseq-accurate-single-cell-rna-seq-quantification-with-bias-correction
#14
Liang Chen, Sika Zheng
With rapid technical advances, single cell RNA-seq (scRNA-seq) has been used to detect cell subtypes exhibiting distinct gene expression profiles and to trace cell transitions in development and disease. However, the potential of scRNA-seq for new discoveries is constrained by the robustness of subsequent data analysis. Here we propose a robust model, BCseq (bias-corrected sequencing analysis), to accurately quantify gene expression from scRNA-seq. BCseq corrects inherent bias of scRNA-seq in a data-adaptive manner and effectively removes technical noise...
April 30, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29714687/synthetic-hormone-responsive-transcription-factors-can-monitor-and-re-program-plant-development
#15
Arjun Khakhar, Alexander R Leydon, Andrew C Lemmex, Eric Klavins, Jennifer L Nemhauser
Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity1,2 . Hormones coordinate these programs, creating chemical circuitry3 that has been represented in mathematical models4,5 ; however, model-guided engineering of plant morphology has been limited by a lack of tools6,7 . Here, we introduce a novel set of synthetic and modular <u>h</u>ormone <u>a</u>ctivated <u>C</u>as9-based <u>r</u>epressors (HACRs) in Arabidopsis thaliana that respond to three hormones: auxin, gibberellins and jasmonates...
May 1, 2018: ELife
https://www.readbyqxmd.com/read/29710372/a-matter-of-phylogenetic-scale-distinguishing-incomplete-lineage-sorting-from-lateral-gene-transfer-as-the-cause-of-gene-tree-discord-in-recent-versus-deep-diversification-histories
#16
L Lacey Knowles, Huateng Huang, Jeet Sukumaran, Stephen A Smith
PREMISE OF THE STUDY: Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i...
April 30, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29709110/making-lineage-decisions-with-biological-noise-lessons-from-the-early-mouse-embryo
#17
REVIEW
Claire S Simon, Anna-Katerina Hadjantonakis, Christian Schröter
Understanding how individual cells make fate decisions that lead to the faithful formation and homeostatic maintenance of tissues is a fundamental goal of contemporary developmental and stem cell biology. Seemingly uniform populations of stem cells and multipotent progenitors display a surprising degree of heterogeneity, primarily originating from the inherent stochastic nature of molecular processes underlying gene expression. Despite this heterogeneity, lineage decisions result in tissues of a defined size and with consistent proportions of differentiated cell types...
April 30, 2018: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/29705632/bursting-onto-the-scene-exploring-stochastic-mrna-production-in-bacteria
#18
REVIEW
Daniel Jones, Johan Elf
Recent large-scale measurements of gene expression variability (or noise) in E. coli have led to the unexpected conclusion that the variability is in large part dictated by and increasing with the mean level of expression. Here we review the evidence for this apparent universal trend in variability, as well as for the related idea that transcription is fundamentally bursty. We examine recently proposed mechanisms for burstiness and universality and argue that they do not explain important features of observed data...
April 26, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29700467/digestion-ligation-only-hi-c-is-an-efficient-and-cost-effective-method-for-chromosome-conformation-capture
#19
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Liang Li, Yijun Ruan, Zhen F Fu, Guoliang Li, Gang Cao
Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments...
April 26, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29696600/high-cooperativity-in-negative-feedback-can-amplify-noisy-gene-expression
#20
Pavol Bokes, Yen Ting Lin, Abhyudai Singh
Burst-like synthesis of protein is a significant source of cell-to-cell variability in protein levels. Negative feedback is a common example of a regulatory mechanism by which such stochasticity can be controlled. Here we consider a specific kind of negative feedback, which makes bursts smaller in the excess of protein. Increasing the strength of the feedback may lead to dramatically different outcomes depending on a key parameter, the noise load, which is defined as the squared coefficient of variation the protein exhibits in the absence of feedback...
April 25, 2018: Bulletin of Mathematical Biology
keyword
keyword
11793
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"