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Computation gene circuits

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https://www.readbyqxmd.com/read/29675221/multiple-advanced-logic-gates-made-of-dna-ag-nanocluster-and-the-application-for-intelligent-detection-of-pathogenic-bacterial-genes
#1
Xiaodong Lin, Yaqing Liu, Jiankang Deng, Yanlong Lyu, Pengcheng Qian, Yunfei Li, Shuo Wang
The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer...
February 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29673480/thalamic-reticular-dysfunction-as-a-circuit-endophenotype-in-neurodevelopmental-disorders
#2
REVIEW
Alexandra Krol, Ralf D Wimmer, Michael M Halassa, Guoping Feng
Diagnoses of behavioral disorders such as autism spectrum disorder and schizophrenia are based on symptomatic descriptions that have been difficult to connect to mechanism. Although psychiatric genetics provide insight into the genetic underpinning of such disorders, with a majority of cases explained by polygenic factors, it remains difficult to design rational treatments. In this review, we highlight the value of understanding neural circuit function both as an intermediate level of explanatory description that links gene to behavior and as a pathway for developing rational diagnostics and therapeutics for behavioral disorders...
April 18, 2018: Neuron
https://www.readbyqxmd.com/read/29614119/computational-analysis-of-the-oscillatory-behavior-at-the-translation-level-induced-by-mrna-levels-oscillations-due-to-finite-intracellular-resources
#3
Yoram Zarai, Tamir Tuller
Recent studies have demonstrated how the competition for the finite pool of available gene expression factors has important effect on fundamental gene expression aspects. In this study, based on a whole-cell model simulation of translation in S. cerevisiae, we evaluate for the first time the expected effect of mRNA levels fluctuations on translation due to the finite pool of ribosomes. We show that fluctuations of a single gene or a group of genes mRNA levels induce periodic behavior in all S. cerevisiae translation factors and aspects: the ribosomal densities and the translation rates of all S...
April 3, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29605929/automated-computational-inference-of-multi-protein-assemblies-from-biochemical-co-purification-data
#4
Florian Goebels, Lucas Hu, Gary Bader, Andrew Emili
Biology has amassed a wealth of information about the function of a multitude of protein-coding genes across species. The challenge now is to understand how all these proteins work together to form a living organism, and a crucial step for gaining this knowledge is a complete description of the molecular "wiring circuits" that underlie cellular processes. In this chapter, we describe a general computational framework for predicting multi-protein assemblies from biochemical co-fractionation data.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29579377/quantitative-investigation-of-the-role-of-intra-inter-cellular-dynamics-in-bacterial-quorum-sensing
#5
Eric Leaman, Brian Q Geuther, Bahareh Behkam
Bacteria utilize diffusible signals to regulate population density-dependent coordinated gene expression in a process called quorum sensing (QS). While the intracellular regulatory mechanisms of QS are well-understood, the effect of spatiotemporal changes in the population configuration on the sensitivity and robustness of the QS response remains largely unexplored. Using a microfluidic device, we quantitatively characterized the emergent behavior of a population of swimming E. coli bacteria engineered with the lux QS system and a GFP reporter...
March 26, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29496145/laser-microdissection-and-gene-expression-profiling-in-the-human-postmortem-brain
#6
Kai-Christian Sonntag, Tsung-Ung W Woo
Laser microdissection in combination with gene expression profiling using postmortem human brain tissue provides a powerful approach to interrogating cell type-specific pathologies within neural circuits that are known to be dysfunctional in neuropsychiatric disorders. The success of these experiments critically depends on a number of factors, such as the cellular purity of the sample, the quality of the RNA, the methodologies of data normalization and computational data analysis, and how data are interpreted...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29437890/brain-transcriptome-databases-a-user-s-guide
#7
Jason M Keil, Adel Qalieh, Kenneth Y Kwan
Transcriptional programs instruct the generation and maintenance of diverse subtypes of neural cells, establishment of distinct brain regions, formation and function of neural circuits, and ultimately behavior. Spatiotemporal and cell type-specific analyses of the transcriptome, the sum total of all RNA transcripts in a cell or an organ, can provide insights into the role of genes in brain development and function, and their potential contribution to disorders of the brain. In the previous decade, advances in sequencing technology and funding from the National Institutes of Health and private foundations for large-scale genomics projects have led to a growing collection of brain transcriptome databases...
February 7, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29401445/simulating-genetic-circuits-in-bacterial-populations-with-growth-heterogeneity
#8
Anjan Roy, Stefan Klumpp
We computationally study genetic circuits in bacterial populations with heterogeneities in the growth rate. To that end, we present a stochastic simulation method for gene circuits in populations of cells and propose an efficient implementation that we call the "Next Family Method". Within this approach, we implement different population setups, specifically Chemostat-type growth and growth in an ideal Mother Machine and show that the population structure and its statistics are different for the different setups whenever there is growth heterogeneity...
January 23, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29371263/tulsa-1000-a-naturalistic-study-protocol-for-multilevel-assessment-and-outcome-prediction-in-a-large-psychiatric-sample
#9
Teresa A Victor, Sahib S Khalsa, W Kyle Simmons, Justin S Feinstein, Jonathan Savitz, Robin L Aupperle, Hung-Wen Yeh, Jerzy Bodurka, Martin P Paulus
INTRODUCTION: Although neuroscience has made tremendous progress towards understanding the basic neural circuitry underlying important processes such as attention, memory and emotion, little progress has been made in applying these insights to psychiatric populations to make clinically meaningful treatment predictions. The overall aim of the Tulsa 1000 (T-1000) study is to use the NIMH Research Domain Criteria framework in order to establish a robust and reliable dimensional set of variables that quantifies the positive and negative valence, cognition and arousal domains, including interoception, to generate clinically useful treatment predictions...
January 24, 2018: BMJ Open
https://www.readbyqxmd.com/read/29258623/dynamic-modeling-of-folliculogenesis-signaling-pathways-in-the-presence-of-mirnas-expression
#10
Abolfazl Bahrami, Seyed Reza Miraie-Ashtiani, Mostafa Sadeghi, Ali Najafi, Reza Ranjbar
BACKGROUND: TEK signaling plays a very important role in folliculogenesis. It activates Ras/ERK/MYC, PI3K/AKT/mTORC1 and ovarian steroidogenesis activation pathways. These are the main pathways for cell growth, differentiation, migration, adhesion, proliferation, survival and protein synthesis. RESULTS: TEK signaling on each of the two important pathways where levels of pERK, pMYC, pAkt, pMCL1 and pEIF4EBP1 are increased in dominant follicles and pMYC is decreased in dominant follicles...
December 19, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29227103/a-robust-molecular-network-motif-for-period-doubling-devices
#11
Christian Cuba Samaniego, Elisa Franco
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune...
January 19, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29200199/programmable-full-adder-computations-in-communicating-three-dimensional-cell-cultures
#12
David Ausländer, Simon Ausländer, Xavier Pierrat, Leon Hellmann, Leila Rachid, Martin Fussenegger
Synthetic biologists have advanced the design of trigger-inducible gene switches and their assembly into input-programmable circuits that enable engineered human cells to perform arithmetic calculations reminiscent of electronic circuits. By designing a versatile plug-and-play molecular-computation platform, we have engineered nine different cell populations with genetic programs, each of which encodes a defined computational instruction. When assembled into 3D cultures, these engineered cell consortia execute programmable multicellular full-adder logics in response to three trigger compounds...
January 2018: Nature Methods
https://www.readbyqxmd.com/read/29163022/the-insula-and-taste-learning
#13
REVIEW
Adonis Yiannakas, Kobi Rosenblum
The sense of taste is a key component of the sensory machinery, enabling the evaluation of both the safety as well as forming associations regarding the nutritional value of ingestible substances. Indicative of the salience of the modality, taste conditioning can be achieved in rodents upon a single pairing of a tastant with a chemical stimulus inducing malaise. This robust associative learning paradigm has been heavily linked with activity within the insular cortex (IC), among other regions, such as the amygdala and medial prefrontal cortex...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29142298/shaping-bacterial-population-behavior-through-computer-interfaced-control-of-individual-cells
#14
Remy Chait, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, Călin C Guet
Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133926/genetic-programs-can-be-compressed-and-autonomously-decompressed-in-live-cells
#15
Nicolas Lapique, Yaakov Benenson
Fundamental computer science concepts have inspired novel information-processing molecular systems in test tubes 1-13 and genetically encoded circuits in live cells 14-21 . Recent research has shown that digital information storage in DNA, implemented using deep sequencing and conventional software, can approach the maximum Shannon information capacity 22 of two bits per nucleotide 23 . In nature, DNA is used to store genetic programs, but the information content of the encoding rarely approaches this maximum 24 ...
November 13, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/29122925/genetic-circuit-characterization-and-debugging-using-rna-seq
#16
Thomas E Gorochowski, Amin Espah Borujeni, Yongjin Park, Alec Ak Nielsen, Jing Zhang, Bryan S Der, D Benjamin Gordon, Christopher A Voigt
Genetic circuits implement computational operations within a cell. Debugging them is difficult because their function is defined by multiple states (e.g., combinations of inputs) that vary in time. Here, we develop RNA-seq methods that enable the simultaneous measurement of: (i) the states of internal gates, (ii) part performance (promoters, insulators, terminators), and (iii) impact on host gene expression. This is applied to a three-input one-output circuit consisting of three sensors, five NOR/NOT gates, and 46 genetic parts...
November 9, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29100073/synaptic-neurexin-complexes-a-molecular-code-for-the-logic-of-neural-circuits
#17
REVIEW
Thomas C Südhof
Synapses are specialized junctions between neurons in brain that transmit and compute information, thereby connecting neurons into millions of overlapping and interdigitated neural circuits. Here, we posit that the establishment, properties, and dynamics of synapses are governed by a molecular logic that is controlled by diverse trans-synaptic signaling molecules. Neurexins, expressed in thousands of alternatively spliced isoforms, are central components of this dynamic code. Presynaptic neurexins regulate synapse properties via differential binding to multifarious postsynaptic ligands, such as neuroligins, cerebellin/GluD complexes, and latrophilins, thereby shaping the input/output relations of their resident neural circuits...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29054289/cross-talk-between-the-epigenome-and-neural-circuits-in-drug-addiction
#18
Philipp Mews, Erin S Calipari
Drug addiction is a behavioral disorder characterized by dysregulated learning about drugs and associated cues that result in compulsive drug seeking and relapse. Learning about drug rewards and predictive cues is a complex process controlled by a computational network of neural connections interacting with transcriptional and molecular mechanisms within each cell to precisely guide behavior. The interplay between rapid, temporally specific neuronal activation, and longer-term changes in transcription is of critical importance in the expression of appropriate, or in the case of drug addiction, inappropriate behaviors...
2017: Progress in Brain Research
https://www.readbyqxmd.com/read/29052539/engineering-diagnostic-and-therapeutic-gut-bacteria
#19
Brian P Landry, Jeffrey J Tabor
Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions...
October 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#20
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
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