Read by QxMD icon Read

Gene noise

Anna-Lena Heins, Dirk Weuster-Botz
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions...
March 14, 2018: Bioprocess and Biosystems Engineering
Leland J Dunwoodie, William L Poehlman, Stephen P Ficklin, Frank Alexander Feltus
Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors...
February 16, 2018: Oncotarget
Takeshi Takamatsu, Marouane Baslam, Takuya Inomata, Kazusato Oikawa, Kimiko Itoh, Takayuki Ohnishi, Tetsu Kinoshita, Toshiaki Mitsui
Chloroplasts, which perform photosynthesis, are one of the most important organelles in green plants and algae. Chloroplasts maintain an independent genome that includes important genes encoding their photosynthetic machinery and various housekeeping functions. Owing to its non-recombinant nature, low mutation rates, and uniparental inheritance, the chloroplast genome (plastome) can give insights into plant evolution and ecology and in the development of biotechnological and breeding applications. However, efficient methods to obtain high-quality chloroplast DNA (cpDNA) are currently not available, impeding powerful sequencing and further functional genomics research...
2018: Frontiers in Plant Science
Hengchao Chen, Yazhi Xing, Li Xia, Zhengnong Chen, Shankai Yin, Jian Wang
The synapse between inner hair cells (IHCs) and type I spiral ganglion neurons (SGNs) has been identified as a sensitive structure to noise-induced damage in the mammalian cochlea. Since this synapse provides the major information pathway from the cochlea to the auditory brain, it is important to maintain its integrity. Neurotrophin-3 (NT-3) has been known to play an important role in the development and the functional maintenance of this synapse. Application of exogenous NT-3, or overexpression of this gene in a transgenic animal model, have shown the value to protect this synapse from noise-induced damage...
March 13, 2018: Gene Therapy
Benjamin Kleeman, Andre Olsson, Tess Newkold, Matt Kofron, Monica DeLay, David Hildeman, H Leighton Grimes
The advent of facile genome engineering technologies has made the generation of knock-in gene-expression or fusion-protein reporters more tractable. Fluorescent protein labeling of specific genes combined with surface marker profiling can more specifically identify a cell population. However, the question of which fluorescent proteins to utilize to generate reporter constructs is made difficult by the number of candidate proteins and the lack of updated experimental data on newer fluorescent proteins. Compounding this problem, most fluorescent proteins are designed and tested for use in microscopy...
March 13, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney
The 3D structure of chromatin plays a key role in genome function, including gene expression, DNA replication, chromosome segregation, and DNA repair. Furthermore the location of genomic loci within the nucleus, especially relative to each other and nuclear structures such as the nuclear envelope and nuclear bodies strongly correlates with aspects of function such as gene expression. Therefore, determining the 3D position of the 6 billion DNA base pairs in each of the 23 chromosomes inside the nucleus of a human cell is a central challenge of biology...
March 9, 2018: PLoS Computational Biology
Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yiwei Liu
BACKGROUND: Recently, researchers have tried to integrate various dynamic information with static protein-protein interaction (PPI) networks to construct dynamic PPI networks. The shift from static PPI networks to dynamic PPI networks is essential to reveal the cellular function and organization. However, it is still impossible to construct an absolutely reliable dynamic PPI networks due to the noise and incompletion of high-throughput experimental data. RESULTS: To deal with uncertain data, some uncertain graph models and theories have been proposed to analyze social networks, electrical networks and biological networks...
October 16, 2017: BMC Genomics
Xiaojian Shao, Ming-An Sun
The level of gene expression is known to vary from cell to cell and even in the same cell over time. This variability provides cells with the ability to mitigate environmental stresses and genetic perturbations, and facilitates gene expression evolution. Recently, many valuable gene expression noise data measured at the single-cell level and gene expression variation measured for cell populations have become available. In this chapter, we show how to perform integrative analysis using these data. Specifically, we introduce how to apply a machine learning technique (support vector regression) to explore the relationship between gene expression variations and stochastic noise...
2018: Methods in Molecular Biology
Tomas Tokar, Chiara Pastrello, Varune R Ramnarine, Chang-Qi Zhu, Kenneth J Craddock, Larrisa A Pikor, Emily A Vucic, Simon Vary, Frances A Shepherd, Ming-Sound Tsao, Wan L Lam, Igor Jurisica
In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions...
February 6, 2018: Oncotarget
Konrad Kadzielawa, Biji Mathew, Clara R Stelman, Arden Zhengdeng Lei, Leianne Torres, Steven Roth
PURPOSE: The pathophysiology of retinal ischemia involves mechanisms including inflammation and apoptosis. Ischemic post-conditioning (Post-C), a brief non-lethal ischemia, induces a long-term ischemic tolerance, but the mechanisms of ischemic post-conditioning in the retina have only been described on a limited basis. Accordingly, we conducted this study to determine the molecular events in retinal ischemic post-conditioning and to identify targets for therapeutic strategies for retinal ischemia...
March 5, 2018: Graefe's Archive for Clinical and Experimental Ophthalmology
Jeffrey N Carey, Erin L Mettert, Manuela Roggiani, Kevin S Myers, Patricia J Kiley, Mark Goulian
Microbial populations can maximize fitness in dynamic environments through bet hedging, a process wherein a subpopulation assumes a phenotype not optimally adapted to the present environment but well adapted to an environment likely to be encountered. Here, we show that oxygen induces fluctuating expression of the trimethylamine oxide (TMAO) respiratory system of Escherichia coli, diversifying the cell population and enabling a bet-hedging strategy that permits growth following oxygen loss. This regulation by oxygen affects the variance in gene expression but leaves the mean unchanged...
February 26, 2018: Cell
Andrew P Landstrom, Ernesto Fernandez, Jill A Rosenfeld, Yaping Yang, Andrew L Dailey-Schwartz, Christina Y Miyake, Hugh D Allen, Daniel J Penny, Jeffrey J Kim
BACKGROUND: Due to rapid expansion of clinical genetic testing, an increasing number of genetic variants of undetermined significance are being identified in children with unclear diagnostic value. Variants found in genes associated with heritable channelopathies, such as long QT syndrome (LQTS), are particularly difficult to interpret given the risk of sudden cardiac death associated with pathologic mutations. OBJECTIVE: To determine whether variants in LQTS-associated genes from whole exome sequencing (WES) represent disease-associated biomarkers or background genetic "noise...
March 1, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
Teppei Noda, Steven J Meas, Jumpei Nogami, Yutaka Amemiya, Ryutaro Uchi, Yasuyuki Ohkawa, Koji Nishimura, Alain Dabdoub
Primary auditory neurons (PANs) play a critical role in hearing by transmitting sound information from the inner ear to the brain. Their progressive degeneration is associated with excessive noise, disease and aging. The loss of PANs leads to permanent hearing impairment since they are incapable of regenerating. Spiral ganglion non-neuronal cells (SGNNCs), comprised mainly of glia, are resident within the modiolus and continue to survive after PAN loss. These attributes make SGNNCs an excellent target for replacing damaged PANs through cellular reprogramming...
2018: Frontiers in Cell and Developmental Biology
Andrew R M Bradbury, Nathan D Trinklein, Holger Thie, Ian C Wilkinson, Atul K Tandon, Stephen Anderson, Catherine L Bladen, Brittany Jones, Shelley Force Aldred, Marco Bestagno, Oscar Burrone, Jennifer Maynard, Fortunato Ferrara, James S Trimmer, Janina Görnemann, Jacob Glanville, Philipp Wolf, Andre Frenzel, Julin Wong, Xin Yu Koh, Hui-Yan Eng, David Lane, Marie-Paule Lefranc, Mike Clark, Stefan Dübel
Monoclonal antibodies are commonly assumed to be monospecific, but anecdotal studies have reported genetic diversity in antibody heavy chain and light chain genes found within individual hybridomas. As the prevalence of such diversity has never been explored, we analyzed 185 random hybridomas, in a large multicenter dataset. The hybridomas analyzed were not biased towards those with cloning difficulties or known to have additional chains. Of the hybridomas we evaluated, 126 (68.1%) contained no additional productive chains, while the remaining 59 (31...
February 27, 2018: MAbs
Erin Hisey, Matthew Gene Kearney, Richard Mooney
The complex skills underlying verbal and musical expression can be learned without external punishment or reward, indicating their learning is internally guided. The neural mechanisms that mediate internally guided learning are poorly understood, but a circuit comprising dopamine-releasing neurons in the midbrain ventral tegmental area (VTA) and their targets in the basal ganglia are important to externally reinforced learning. Juvenile zebra finches copy a tutor song in a process that is internally guided and, in adulthood, can learn to modify the fundamental frequency (pitch) of a target syllable in response to external reinforcement with white noise...
February 26, 2018: Nature Neuroscience
Georges Goetz, Tong Ling, Tushar Gupta, Seungbum Kang, Jenny Wang, Patrick D Gregory, B Hyle Park, Daniel Palanker
Optical phase changes induced by transient perturbations provide a sensitive measure of material properties. We demonstrate the high sensitivity and speed of such methods, using two interferometric techniques: quantitative phase imaging (QPI) in transmission and phase-resolved optical coherence tomography (OCT) in reflection. Shot-noise-limited QPI can resolve energy deposition of about 3.4 mJ/cm2 in a single pulse, which corresponds to 0.8 °C temperature rise in a single cell. OCT can detect deposition of 24 mJ/cm2 energy between two scattering interfaces producing signals with about 30-dB signal-to-noise ratio (SNR), and 4...
February 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
Stilianos Louca, Michael Doebeli, Laura Wegener Parfrey
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases...
February 26, 2018: Microbiome
Vakil Takhaveev, Matthias Heinemann
In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations...
February 21, 2018: Current Opinion in Microbiology
Sarangam Majumdar, Sukla Pal
Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication...
February 23, 2018: Journal of Cell Communication and Signaling
Oluwatosin Oluwadare, Yuxiang Zhang, Jianlin Cheng
BACKGROUND: The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function...
February 23, 2018: BMC Genomics
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"