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https://www.readbyqxmd.com/read/28209736/pejvakin-a-candidate-stereociliary-rootlet-protein-regulates-hair-cell-function-in-a-cell-autonomous-manner
#1
Marcin Kazmierczak, Piotr Kazmierczak, Anthony W Peng, Suzan L Harris, Prahar Shah, Jean-Luc Puel, Marc Lenoir, Santos J Franco, Martin Schwander
Mutations in the Pejvakin (PJVK) gene are thought to cause auditory neuropathy and hearing loss of cochlear origin by affecting noise-induced peroxisome proliferation in auditory hair cells and neurons. Here we demonstrate that loss of pejvakin in hair cells, but not in neurons, causes profound hearing loss and outer hair cell degeneration in mice. Pejvakin binds to and co-localizes with the rootlet component TRIOBP at the base of stereocilia in injectoporated hair cells, a pattern that is disrupted by deafness-associated PJVK mutations...
February 16, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28208333/stochastic-liouville-equation-for-particles-driven-by-dichotomous-environmental-noise
#2
Paul C Bressloff
We analyze the stochastic dynamics of a large population of noninteracting particles driven by a global environmental input in the form of a dichotomous Markov noise process (DMNP). The population density of particle states evolves according to a stochastic Liouville equation with respect to different realizations of the DMNP. We then exploit the connection with previous work on diffusion in randomly switching environments, in order to derive moment equations for the distribution of solutions to the stochastic Liouville equation...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28192413/evolution-of-a-split-rna-polymerase-as-a-versatile-biosensor-platform
#3
Jinyue Pu, Julia Zinkus-Boltz, Bryan C Dickinson
Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE)...
February 13, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28186903/construction-of-refined-protein-interaction-network-for-predicting-essential-proteins
#4
Min Li, Peng Ni, Xiaopei Chen, Jianxin Wang, Fangxiang Wu, Yi Pan
Identification of essential proteins based on protein interaction network (PIN) is a very important and hot topic in the post genome era. Up to now, a number of network-based essential protein discovery methods have been proposed. Generally, a static protein interaction network was constructed by using the protein-protein interactions obtained from different experiments or databases. Unfortunately, most of the network-based essential protein discovery methods are sensitive to the reliability of the constructed PIN...
February 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28183729/organelles-understanding-noise-and-heterogeneity-in-cell-biology-at-an-intermediate-scale
#5
REVIEW
Amy Y Chang, Wallace F Marshall
Many studies over the years have shown that non-genetic mechanisms for producing cell-to-cell variation can lead to highly variable behaviors across genetically identical populations of cells. Most work to date has focused on gene expression noise as the primary source of phenotypic heterogeneity, yet other sources may also contribute. In this Commentary, we explore organelle-level heterogeneity as a potential secondary source of cellular 'noise' that contributes to phenotypic heterogeneity. We explore mechanisms for generating organelle heterogeneity and present evidence of functional links between organelle morphology and cellular behavior...
February 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28182740/polymorphisms-of-heat-shock-protein-70-genes-hspa1a-hspa1b-and-hspa1l-and-susceptibility-of-noise-induced-hearing-loss-in-a-chinese-population-a-case-control-study
#6
Yanhong Li, Shanfa Yu, Guizhen Gu, Guoshun Chen, Yuxin Zheng, Jie Jiao, Wenhui Zhou, Hui Wu, Zengrui Zhang, Huanling Zhang, Lihua He, Qiuyue Yang, Xiangrong Xu
Noise-induced hearing loss (NIHL) is the second-most frequent form of sensorineural hearing loss. When exposed to the same noise, some workers develop NIHL while others do not, suggesting that NIHL may be associated with genetic factors. To explore the relationship between single nucleotide polymorphisms (SNPs) in heat shock protein 70 (HSP70) genes (HSPA1A, HSPA1B and HSPA1L) and susceptibility to NIHL in Han Chinese workers exposed to noise, a case-control association study was carried out with 286 hearing loss cases and 286 matched with gender, age, type of work, and exposure time, drawn from a population of 3790 noise-exposed workers...
2017: PloS One
https://www.readbyqxmd.com/read/28182661/representing-high-throughput-expression-profiles-via-perturbation-barcodes-reveals-compound-targets
#7
Tracey M Filzen, Peter S Kutchukian, Jeffrey D Hermes, Jing Li, Matthew Tudor
High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations. As profiling campaigns expand in scope, it is important to homogenize, summarize, and analyze the resulting data in a manner that captures significant biological signals in spite of various noise sources such as batch effects and stochastic variation. We used the L1000 platform for large-scale profiling of 978 representative genes across thousands of compound treatments...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28176840/the-dynamic-mechanism-of-noisy-signal-decoding-in-gene-regulation
#8
Peijiang Liu, Haohua Wang, Lifang Huang, Tianshou Zhou
Experimental evidence supports that signaling pathways can induce different dynamics of transcription factor (TF) activation, but how an input signal is encoded by such a dynamic, noisy TF and further decoded by downstream genes remains largely unclear. Here, using a system of stochastic transcription with signal regulation, we show that (1) keeping the intensity of the signal noise invariant but prolonging the signal duration can both enhance the mutual information (MI) and reduce the energetic cost (EC); (2) if the signal duration is fixed, the larger MI needs the larger EC, but if the signal period is fixed, there is an optimal time that the signal spends at one lower branch, such that MI reaches the maximum; (3) if both the period and the duration are simultaneously fixed, increasing the input noise can always enhance MI in the case of transcription regulation rather than in the case of degradation regulation...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166866/genetic-control-of-encoding-strategy-in-a-food-sensing-neural-circuit
#9
Giovanni Diana, Dhaval S Patel, Eugeni V Entchev, Mei Zhan, Hang Lu, QueeLim Ch'ng
Neuroendocrine circuits encode environmental information via changes in gene expression and other biochemical activities to regulate physiological responses. Previously, we showed that daf-7 TGFβ and tph-1 tryptophan hydroxylase expression in specific neurons encode food abundance to modulate lifespan in Caenorhabditis elegans, and uncovered cross- and self-regulation among these genes (Entchev et al., 2015). Here, we now extend these findings by showing that these interactions between daf-7 and tph-1 regulate redundancy and synergy among neurons in food encoding through coordinated control of circuit-level signal and noise properties...
February 7, 2017: ELife
https://www.readbyqxmd.com/read/28165493/a-noise-trimming-and-positional-significance-of-transposon-insertion-system-to-identify-essential-genes-in-yersinia-pestis
#10
Zheng Rong Yang, Helen L Bullifent, Karen Moore, Konrad Paszkiewicz, Richard J Saint, Stephanie J Southern, Olivia L Champion, Nicola J Senior, Mitali Sarkar-Tyson, Petra C F Oyston, Timothy P Atkins, Richard W Titball
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28158291/recursive-random-forest-algorithm-for-constructing-multilayered-hierarchical-gene-regulatory-networks-that-govern-biological-pathways
#11
Wenping Deng, Kui Zhang, Victor Busov, Hairong Wei
BACKGROUND: Present knowledge indicates a multilayered hierarchical gene regulatory network (ML-hGRN) often operates above a biological pathway. Although the ML-hGRN is very important for understanding how a pathway is regulated, there is almost no computational algorithm for directly constructing ML-hGRNs. RESULTS: A backward elimination random forest (BWERF) algorithm was developed for constructing the ML-hGRN operating above a biological pathway. For each pathway gene, the BWERF used a random forest model to calculate the importance values of all transcription factors (TFs) to this pathway gene recursively with a portion (e...
2017: PloS One
https://www.readbyqxmd.com/read/28157766/effect-of-interaction-between-noise-and-a1166c-site-of-at1r-gene-polymorphism-on-essential-hypertension-in-an-iron-and-steel-enterprise-workers
#12
Junwang Tong, Ying Wang, Juxiang Yuan, Jingbo Yang, Zhaoyang Wang, Yao Zheng, Feng Chai, Xiangwen Li
OBJECTIVE: This study aimed to analyze the interaction of Angiotensin II type 1 receptor (AT1R) gene polymorphism and occupational noise on the occurrence of essential hypertension (EH) in steel and iron enterprise men workers. METHODS: A case control study of 935 iron and steel enterprise men workers was conducted, which included 312 cases of hypertension and 623 cases without hypertension. The noise at the workplace was assessed. Polymorphism of AT1R of the workers was examined using polymerase chain reaction - restriction fragment length polymorphism...
February 2, 2017: Journal of Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28153040/bicpams-software-for-biological-data-analysis-with-pattern-based-biclustering
#13
Rui Henriques, Francisco L Ferreira, Sara C Madeira
BACKGROUND: Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters...
February 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28137253/the-integration-of-weighted-human-gene-association-networks-based-on-link-prediction
#14
Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang, Jing Zhao
BACKGROUND: Physical and functional interplays between genes or proteins have important biological meaning for cellular functions. Some efforts have been made to construct weighted gene association meta-networks by integrating multiple biological resources, where the weight indicates the confidence of the interaction. However, it is found that these existing human gene association networks share only quite limited overlapped interactions, suggesting their incompleteness and noise. RESULTS: Here we proposed a workflow to construct a weighted human gene association network using information of six existing networks, including two weighted specific PPI networks and four gene association meta-networks...
January 31, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28135279/cell-sorting-and-noise-induced-cell-plasticity-coordinate-to-sharpen-boundaries-between-gene-expression-domains
#15
Qixuan Wang, William R Holmes, Julian Sosnik, Thomas Schilling, Qing Nie
A fundamental question in biology is how sharp boundaries of gene expression form precisely in spite of biological variation/noise. Numerous mechanisms position gene expression domains across fields of cells (e.g. morphogens), but how these domains are refined remains unclear. In some cases, domain boundaries sharpen through differential adhesion-mediated cell sorting. However, boundaries can also sharpen through cellular plasticity, with cell fate changes driven by up- or down-regulation of gene expression...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28134382/measurement-of-bistability-in-a-multidimensional-parameter-space
#16
Vincent Jaquet, Chieh Hsu, Attila Becskei
Bistability plays an important role to generate two stable states for alternative cell fates, or to promote cellular diversity and cell cycle oscillations. Positive feedback loops are necessary for the existence of bistability and ultrasensitive reactions in the loops broaden the parameter range of bistability. The broader parameter range a system's bistability covers, the more robust the two states are. It is challenging to determine the bistable range of a parameter because noise and transient processes induce transitions between the two states...
January 30, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28122427/familiar-hyperekplexia-a-potential-cause-of-cautious-gait-a-new-korean-case-and-a-systematic-review-of-phenotypes
#17
Yoonju Lee, Nan Young Kim, Sangkyoon Hong, Su Jin Chung, Seong Ho Jeong, Phil Hyu Lee, Young H Sohn
Familial hyperekplexia, also called startle disease, is a rare neurological disorder characterized by excessive startle responses to noise or touch. It can be associated with serious injury from frequent falls, apnea spells, and aspiration pneumonia. Familial hyperekplexia has a heterogeneous genetic background with several identified causative genes; it demonstrates both dominant and recessive inheritance in the α1 subunit of the glycine receptor (GLRA1), the β subunit of the glycine receptor and the presynaptic sodium and chloride-dependent glycine transporter 2 genes...
January 2017: Journal of Movement Disorders
https://www.readbyqxmd.com/read/28114903/a-systematic-comparative-evaluation-of-biclustering-techniques
#18
Victor A Padilha, Ricardo J G B Campello
BACKGROUND: Biclustering techniques are capable of simultaneously clustering rows and columns of a data matrix. These techniques became very popular for the analysis of gene expression data, since a gene can take part of multiple biological pathways which in turn can be active only under specific experimental conditions. Several biclustering algorithms have been developed in the past recent years. In order to provide guidance regarding their choice, a few comparative studies were conducted and reported in the literature...
January 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28114387/gene-expression-noise-enhances-robust-organization-of-the-early-mammalian-blastocyst
#19
William R Holmes, Nabora Soledad Reyes de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie
A critical event in mammalian embryo development is construction of an inner cell mass surrounded by a trophoectoderm (a shell of cells that later form extraembryonic structures). We utilize multi-scale, stochastic modeling to investigate the design principles responsible for robust establishment of these structures. This investigation makes three predictions, each supported by our quantitative imaging. First, stochasticity in the expression of critical genes promotes cell plasticity and has a critical role in accurately organizing the developing mouse blastocyst...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28113451/active-clustering-with-model-based-uncertainty-reduction
#20
Caiming Xiong, David M Johnson, Jason J Corso
Semi-supervised clustering seeks to augment traditional clustering methods by incorporating side information provided via human expertise in order to increase the semantic meaningfulness of the resulting clusters. However, most current methods are passive in the sense that the side information is provided beforehand and selected randomly. This may require a large number of constraints, some of which could be redundant, unnecessary, or even detrimental to the clustering results. Thus in order to scale such semi-supervised algorithms to larger problems it is desirable to pursue an active clustering method- i...
March 9, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
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