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Gene noise

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https://www.readbyqxmd.com/read/28337978/microrna-filters-hox-temporal-transcription-noise-to-confer-boundary-formation-in-the-spinal-cord
#1
Chung-Jung Li, Tian Hong, Ying-Tsen Tung, Ya-Ping Yen, Ho-Chiang Hsu, Ya-Lin Lu, Mien Chang, Qing Nie, Jun-An Chen
The initial rostrocaudal patterning of the neural tube leads to differential expression of Hox genes that contribute to the specification of motor neuron (MN) subtype identity. Although several 3' Hox mRNAs are expressed in progenitors in a noisy manner, these Hox proteins are not expressed in the progenitors and only become detectable in postmitotic MNs. MicroRNA biogenesis impairment leads to precocious expression and propagates the noise of Hoxa5 at the protein level, resulting in an imprecise Hoxa5-Hoxc8 boundary...
March 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28337537/is-prepulse-modification-altered-by-continuous-theta-burst-stimulation-dat1-genotype-and-motor-threshold-interact-on-prepulse-modification-following-brain-stimulation
#2
S Notzon, N Vennewald, A Gajewska, A L Klahn, J Diemer, B Winter, I Fohrbeck, V Arolt, P Pauli, K Domschke, P Zwanzger
Previous studies suggest an inhibitory top-down control of the amygdala by the prefrontal cortex (PFC). Both brain regions play a role in the modulation of prepulse modification (PPM) of the acoustic startle response by a pre-stimulus. Repetitive transcranial magnetic stimulation (rTMS) can modulate the activity of the PFC and might thus affect PPM. This study tested the effect of inhibitory rTMS on PPM accounting for a genetic variant of the dopamine transporter gene (DAT1). Healthy participants (N = 102) were stimulated with continuous theta burst stimulation (cTBS, an intense form of inhibitory rTMS) or sham treatment over the right PFC...
March 24, 2017: European Archives of Psychiatry and Clinical Neuroscience
https://www.readbyqxmd.com/read/28335761/the-effects-of-jiao-tai-wan-on-sleep-inflammation-and-insulin-resistance-in-obesity-resistant-rats-with-chronic-partial-sleep-deprivation
#3
Xin Zou, Wenya Huang, Fuer Lu, Ke Fang, Dingkun Wang, Shuyong Zhao, Jiming Jia, Lijun Xu, Kaifu Wang, Nan Wang, Hui Dong
BACKGROUND: Jiao-Tai-Wan (JTW), composed of Rhizome Coptidis and Cortex Cinnamomi, is a classical traditional Chinese prescription for treating insomnia. Several in vivo studies have concluded that JTW could exert its therapeutical effect in insomnia rats. However, the specific mechanism is still unclear. The present study aimed to explore the effect of JTW on sleep in obesity-resistant (OR) rats with chronic partial sleep deprivation (PSD) and to clarify its possible mechanism. METHODS: JTW was prepared and the main components contained in the granules were identified by 3D-High Performance Liquid Chromatography (3D-HPLC) assay...
March 23, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28333948/epigenomic-annotation-of-noncoding-mutations-identifies-mutated-pathways-in-primary-liver-cancer
#4
Rebecca F Lowdon, Ting Wang
Evidence that noncoding mutation can result in cancer driver events is mounting. However, it is more difficult to assign molecular biological consequences to noncoding mutations than to coding mutations, and a typical cancer genome contains many more noncoding mutations than protein-coding mutations. Accordingly, parsing functional noncoding mutation signal from noise remains an important challenge. Here we use an empirical approach to identify putatively functional noncoding somatic single nucleotide variants (SNVs) from liver cancer genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28329261/effects-of-noise-on-vascular-function-oxidative-stress-and-inflammation-mechanistic-insight-from-studies-in-mice
#5
Thomas Münzel, Andreas Daiber, Sebastian Steven, Lan P Tran, Elisabeth Ullmann, Sabine Kossmann, Frank P Schmidt, Matthias Oelze, Ning Xia, Huige Li, Antonio Pinto, Philipp Wild, Kai Pies, Erwin R Schmidt, Steffen Rapp, Swenja Kröller-Schön
Aims: Epidemiological studies indicate that traffic noise increases the incidence of coronary artery disease, hypertension and stroke. The underlying mechanisms remain largely unknown. Field studies with nighttime noise exposure demonstrate that aircraft noise leads to vascular dysfunction, which is markedly improved by vitamin C, suggesting a key role of oxidative stress in causing this phenomenon. Methods and results: We developed a novel animal model to study the vascular consequences of aircraft noise exposure...
February 17, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28320972/sensing-relative-signal-in-the-tgf-%C3%AE-smad-pathway
#6
Christopher L Frick, Clare Yarka, Harry Nunns, Lea Goentoro
How signaling pathways function reliably despite cellular variation remains a question in many systems. In the transforming growth factor-β (Tgf-β) pathway, exposure to ligand stimulates nuclear localization of Smad proteins, which then regulate target gene expression. Examining Smad3 dynamics in live reporter cells, we found evidence for fold-change detection. Although the level of nuclear Smad3 varied across cells, the fold change in the level of nuclear Smad3 was a more precise outcome of ligand stimulation...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28315318/development-of-a-liquid-chromatography-mass-spectrometry-based-enzyme-activity-assay-for-phosphatidylcholine-specific-phospholipase-c
#7
Chiaki Murakami, Satoru Mizuno, Sayaka Kado, Fumio Sakane
Phosphatidylcholine (PC)-specific phospholipase C (PC-PLC) hydrolyzes PC to generate the second messenger 1,2-diacylglycerol (DG) and phosphocholine. PC-PLC plays pivotal roles in inflammation, carcinogenesis, tumor progression, atherogenesis, and subarachnoid hemorrhage. Although the activity of PC-PLC in mammalian tissues was discovered approximately 40 years ago, neither the protein nor its gene has been identified. In the present study, we developed a non-radioactive enzyme activity assay for PC-PLC based on mass spectrometric detection of DG following HPLC separation...
March 14, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28315023/external-noise-and-external-signal-induced-transition-of-gene-switch-and-coherence-resonance-in-the-genetic-regulatory-system
#8
Jian-Cheng Shi, Min Luo, Tao Dong, Chu-Sheng Huang
The transition of gene switch induced by external noises (multiplicative external noise and additive external noise) and external signals is investigated in the genetic regulatory system. Results show that the state-to-state transition of gene switch as well as resonant behaviors, such as the explicit coherence resonance (ECR), implicit coherence resonance (ICR) and control parameter coherence biresonance (CPCBR), can appear when noises are injected into the genetic regulatory system. The ECR is increased with the increase of the control parameter value when starting from the supercritical Hopf bifurcation parameter point, and there exists a critical control parameter value for the occurrence of ECR...
March 17, 2017: Acta Biotheoretica
https://www.readbyqxmd.com/read/28306650/cochlear-transcriptome-following-acoustic-trauma-and-dexamethasone-administration-identified-by-a-combination-of-rna-seq-and-dna-microarray
#9
Yukihide Maeda, Ryotaro Omichi, Akiko Sugaya, Shin Kariya, Kazunori Nishizaki
AIM: To elucidate molecular mechanisms of noise-induced hearing loss (NIHL) and glucocorticoid therapy in the cochlea. BACKGROUND: Glucocorticoids are used to treat many forms of acute sensorineural hearing loss, but their molecular action in the cochlea remains poorly understood. METHODS: Dexamethasone was administered intraperitoneally immediately following acoustic overstimulation at 120 dB SPL for 2 hours to mice. The whole cochlear transcriptome was analyzed 12 and 24 hours following noise trauma and dexamethasone administration by both next-generation sequencing (RNA-seq) and DNA microarray...
March 16, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28303531/comprehensive-analysis-of-mile-gene-expression-data-set-advances-discovery-of-leukaemia-type-and-subtype-biomarkers
#10
Wojciech Labaj, Anna Papiez, Andrzej Polanski, Joanna Polanska
Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study...
March 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28295030/plarmeb-integration-of-least-angle-regression-with-empirical-bayes-for-multilocus-genome-wide-association-studies
#11
J Zhang, J-Y Feng, Y-L Ni, Y-J Wen, Y Niu, C L Tamba, C Yue, Q Song, Y-M Zhang
Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise...
March 15, 2017: Heredity
https://www.readbyqxmd.com/read/28294630/peak-integrating-curated-and-noisy-prior-knowledge-in-gene-regulatory-network-inference
#12
Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S Heath
With abundance of biological data, computational prediction of gene regulatory networks (GRNs) from gene expression data has become more feasible. Although incorporating other prior knowledge (PK), along with gene expression data, greatly improves prediction accuracy, the overall accuracy is still low. PK in GRN inference can be categorized into noisy and curated. In noisy PK, relations between genes do not necessarily correspond to regulatory relations and are thus considered inaccurate by inference algorithms such as transcription factor binding and protein-protein interactions...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294287/learning-gene-regulatory-networks-from-next-generation-sequencing-data
#13
Bochao Jia, Suwa Xu, Guanghua Xiao, Vishal Lamba, Faming Liang
In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network...
March 10, 2017: Biometrics
https://www.readbyqxmd.com/read/28292353/the-effect-of-pcdh15-gene-variations-on-the-risk-of-noise-induced-hearing-loss-in-a-chinese-population
#14
Xiang Rong Xu, Jing Jing Wang, Qiu Yue Yang, Jie Jiao, Li Hua He, Shan Fa Yu, Gui Zhen Gu, Guo Shun Chen, Wen Hui Zhou, Hui Wu, Yan Hong Li, Huan Ling Zhang, Zeng Rui Zhang, Xian Ning Jin
Noise-induced hearing loss (NIHL) is a complex disease caused by interactions between environmental and genetic factors. This study investigated whether genetic variability in protocadherin related 15 (PCDH15) underlies an increased susceptibility to the development of NIHL in a Chinese population. The results showed that compared with the TT genotype of rs11004085, CT/CC genotypes were associated with an increased risk of NIHL [adjusted odds ratio (OR) = 2.64; 95% confidence interval (CI): 1.14-6.11, P = 0...
February 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28289731/deblur-rapidly-resolves-single-nucleotide-community-sequence-patterns
#15
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Evguenia Kopylova, James T Morton, Zhenjiang Zech Xu, Eric P Kightley, Luke R Thompson, Embriette R Hyde, Antonio Gonzalez, Rob Knight
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms...
March 2017: MSystems
https://www.readbyqxmd.com/read/28288800/determining-the-limitations-and-benefits-of-noise-in-gene-regulation-and-signal-transduction-through-single-cell-microscopy-based-analysis
#16
REVIEW
Marie D Harton, Eric Batchelor
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review we focus on single cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise...
March 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28287544/single-cell-gene-expression-profiling-using-facs-and-qpcr-with-internal-standards
#17
Joshua R Porter, William G Telford, Eric Batchelor
Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those populations. Single-cell gene expression measurements can help assess the role of noise in gene expression, identify correlations in the expression of pairs of genes, and reveal subpopulations of cells that respond differently to a stimulus. Here, we describe a procedure to measure the expression of up to 96 genes in single mammalian cells isolated from a population growing in tissue culture...
February 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28286046/rudimentary-expression-of-ryamide-in-drosophila-melanogaster-relative-to-other-drosophila-species-points-to-a-functional-decline-of-this-neuropeptide-gene
#18
Jan A Veenstra, Hela Khammassi
RYamides are arthropod neuropeptides with unknown function. In 2011 two RYamides were isolated from D. melanogaster as the ligands for the G-protein coupled receptor CG5811. The D. melanogaster gene encoding these neuropeptides is highly unusual, as there are four RYamide encoding exons in the current genome assembly, but an exon encoding a signal peptide is absent. Comparing the D. melanogaster gene structure with those from other species, including D. virilis, suggests that the gene is degenerating. RNAseq data from 1634 short sequence read archives at NCBI containing more than 34 billion spots yielded numerous individual spots that correspond to the RYamide encoding exons, of which a large number include the intron-exon boundary at the start of this exon...
March 7, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28281689/an-innovative-application-of-time-domain-spectroscopy-on-localized-surface-plasmon-resonance-sensing
#19
Meng-Chi Li, Ying-Feng Chang, Huai-Yi Wang, Yu-Xen Lin, Chien-Cheng Kuo, Ja-An Annie Ho, Cheng-Chung Lee, Li-Chen Su
White-light scanning interferometry (WLSI) is often used to study the surface profiles and properties of thin films because the strength of the technique lies in its ability to provide fast and high resolution measurements. An innovative attempt is made in this paper to apply WLSI as a time-domain spectroscopic system for localized surface plasmon resonance (LSPR) sensing. A WLSI-based spectrometer is constructed with a breadboard of WLSI in combination with a spectral centroid algorithm for noise reduction and performance improvement...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28280462/the-role-of-glia-in-the-peripheral-and-central-auditory-system-following-noise-overexposure-contribution-of-tnf-%C3%AE-and-il-1%C3%AE-to-the-pathogenesis-of-hearing-loss
#20
Verónica Fuentes-Santamaría, Juan Carlos Alvarado, Pedro Melgar-Rojas, María C Gabaldón-Ull, Josef M Miller, José M Juiz
Repeated noise exposure induces inflammation and cellular adaptations in the peripheral and central auditory system resulting in pathophysiology of hearing loss. In this study, we analyzed the mechanisms by which noise-induced inflammatory-related events in the cochlea activate glial-mediated cellular responses in the cochlear nucleus (CN), the first relay station of the auditory pathway. The auditory function, glial activation, modifications in gene expression and protein levels of inflammatory mediators and ultrastructural changes in glial-neuronal interactions were assessed in rats exposed to broadband noise (0...
2017: Frontiers in Neuroanatomy
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